Detecting fetal chromosomal abnormalities using tandem single nucleotide polymorphisms

ABSTRACT

The invention provides tandem single nucleotide polymorphisms and methods for their use, for example, in diagnosing Down Syndrome.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. Ser. No. 12/689,924, filedJan. 19, 2010, which is a continuation-in-part of U.S. patentapplication Ser. No. 11/713,069, filed Feb. 28, 2007 (now U.S. Pat. No.7,799,531, issued Sep. 21, 2010), which claims the benefit of priorityof U.S. Provisional Patent Application No. 60/777,865, filed Feb. 28,2006, each of which is hereby incorporated by reference in its entirety.

BACKGROUND

About 6.4 million women become pregnant in the U.S. each year, and about70% of those women have maternal serum screening and/or an ultrasoundtest in an attempt to determine risks for common birth defects, such asthose resulting from trisomy 13, 18, and 21 (Down Syndrome). Both thesensitivity and specificity of these common non-invasive screening toolsare extremely poor. The best current non-invasive tests lead to a falsepositive rate between 7 and 20%. This high false positive rate has twocatastrophic consequences for American families and society. First, itcreates a large market for the two invasive diagnostic tests, chorionicvillus sampling (CVS) and amniocentesis, which each carry a fetal lossrate of 0.5%-1%. These invasive tests directly result in the loss ofthousands of normal fetuses annually. Second, the high false positiverate heightens maternal anxiety and stress in the large and fixedproportion of pregnant American women who receive false positiveresults. However, prenatal diagnosis are critical in managing apregnancy with chromosomal abnormalities and localized geneticabnormalities, as the diagnosis can allow for interventional care duringdelivery and can prevent devastating consequences for the neonate.Non-invasive tests that rely on detection of short tandem repeat (STR)sequences and low complexity regions have low-sensitivity and are oftenriddled with false-positives and false-negatives. STR sequences and lowcomplexity regions are highly susceptible to polymerase-induced stuttersand therefore generate significant PCR-induced noise. This highbackground noise makes the detection and accurate quantification of lowconcentrations of fetal DNA in maternal plasma very unlikely, makingthese poor markers for use in non-invasive tests for fetal chromosomalabnormalities. Thus there is a tremendous need for the development of asensitive and specific non-invasive test for chromosomal abnormalities,e.g., for prenatal diagnostics.

SUMMARY OF CERTAIN EMBODIMENTS OF THE INVENTION

Accordingly, certain embodiments of the present invention provide amethod for determining whether a fetus has at least one chromosomalabnormality, comprising using tandem single nucleotide polymorphisms tocompare fetal DNA to maternal DNA so as to determine whether the fetushas at least one chromosomal abnormality.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 depicts an example of a tandem SNP.

FIG. 2 depicts a DNA melting map of a constant denaturant capillaryelectrophoresis target sequence covering a tandem SNP.

FIG. 3 depicts an example of a constant denaturant capillaryelectrophoresis electropherogram output. Each peak in these graphsrepresents the number of molecules of each allele for a marker detectedin a sample. FIG. 3A illustrates the output that may result from amaternal buccal swab, which will comprise maternal nucleic acids but nofetal nucleic acids (upper graphs), and from a sample comprising fetalDNA but no maternal DNA, where the fetus has trisomy (lower graphs). Asshown in FIG. 3A, a maternal buccal swab would be expected to show a 1:1ratio for markers for which the maternal genome is heterozygous. Thelower graphs in FIG. 3A illustrate that fetal output would show a ratioof 1:1:1 or 2:1. FIG. 3B illustrates the output that results from asample comprising both maternal and fetal nucleic acids, where the fetushas trisomy. In this case, the output will either show two peaks ofequal area and a third smaller peak or three peaks with different areas,where the areas are in a ratio of peak:x:peak+2x, where “x” representsthe number of molecules of the allele inherited by the fetus from thefather.

FIG. 3C illustrates the output that results from a sample comprisingboth maternal and fetal nucleic acids, where the fetus is normal. Again,three alleles will be detected, and the peaks will be of differentareas, but in this situation, the ratio of the peaks will bepeak:x:peak+x.

DETAILED DESCRIPTION

For years, it has been hoped that the use of fetal cells in maternalblood might be used to assess the genetic status of a developing embryo.Unfortunately, the extremely small amount of fetal cells in maternalblood (about 1 cell per ml) has proven a difficult obstacle to overcomewhen trying to isolate these cells for widespread clinical testing.However, cell-free fetal DNA is present in circulating maternal serum athigher percentages than fetal cells and has the potential to be assessedfor chromosomal or gene defects. Cell-free fetal DNA can range from1-47% of total DNA in maternal blood. However, a critical limitationthat has yet to be successfully overcome is that maternal DNAcontamination makes it difficult to differentiate fetal from maternalDNA.

As described herein, this limitation has been overcome by identifyingtandem single nucleotide polymorphisms (SNPs) to detect chromosomes,e.g., to detect fetal chromosomal abnormalities. The tandem SNPs arecombined with a sensitive DNA separation technology, e.g., high-fidelityPCR and constant denaturant capillary electrophoresis (CDCE), to detectfetal chromosomal abnormalities, e.g., through the simple sampling andcomparison of maternal DNA to fetal DNA, e.g., from maternal serum andmaternal buccal swabs. This approach substantially eliminates falsepositives and significantly reduces false negatives.

Accordingly, certain embodiments of the present invention provide amethod for determining whether a fetus has at least one chromosomalabnormality, comprising using tandem single nucleotide polymorphisms tocompare fetal DNA to maternal DNA so as to determine whether the fetushas at least one chromosomal abnormality.

In certain embodiments of the invention, fetal DNA is obtained frommaternal blood. In certain embodiments of the invention, fetal DNA iscell-free fetal DNA. In certain embodiments of the invention, maternalDNA is obtained from a biological sample, e.g., maternal blood. Incertain embodiments of the invention, maternal DNA is obtained from abuccal swab. In certain embodiments of the invention, maternal DNA isobtained from a biological sample that does not comprise fetal DNA.

In certain embodiments of the invention, fetal DNA is obtained frommaternal blood, maternal urine, maternal sweat, maternal cells, or cellfree DNA from the mother.

In certain embodiments, the biological sample is biological fluid. Incertain embodiments, the biological sample is a maternal biologicalsample. In certain embodiments, samples may be whole blood, bone marrow,blood spots, blood serum, blood plasma, buffy coat preparations, saliva,cerebrospinal fluid, buccal swabs, solid tissues such as skin and hair,body waste products, such as feces and urine. In other embodiments,samples may be lysates, homogenates, or partially purified samples ofbiological materials. In other instances, biological materials caninclude crude or partially purified mixtures of nucleic acids. Incertain embodiments, the biological sample is serum, urine, sweat,cells, or cell free DNA.

In certain embodiments of the invention, the comparison step comprisesusing high-fidelity PCR and constant denaturant capillaryelectrophoresis to compare the fetal DNA to maternal DNA. In certainembodiments of the invention, the comparison step comprises using atleast about 96 tandem single nucleotide polymorphisms.

In certain embodiments of the invention, the method further comprisesthe step of converting the nucleic acid molecules to a homoduplex state,as opposed to being in heteroduplex form. This can be accomplished,e.g., by using an excess of primers and can aid in the tandem SNPanalysis.

In certain embodiments of the invention, methods such as mutationdetection technologies can be used to analyze the tandem SNPs. Incertain embodiments of the invention, methods such as denaturing HPLC,denaturing capillary electrophoresis, cycling temperature capillaryelectrophoresis, allele-specific PCRs, quantitative real time PCRapproaches such as TaqMan® PCR system, polony PCR approaches, andmicroarray approaches can be used to analyze the tandem SNPs.

In certain embodiments of the invention, the single nucleotidepolymorphisms in each tandem single nucleotide polymorphism are each atmost about 250 basepairs apart. In certain embodiments of the invention,the single nucleotide polymorphisms in each tandem single nucleotidepolymorphism are each at most about 200 basepairs apart. In certainembodiments of the invention, the single nucleotide polymorphisms ineach tandem single nucleotide polymorphism are each at most about 150basepairs apart. In certain embodiments of the invention, the singlenucleotide polymorphisms in each tandem single nucleotide polymorphismare each at most about 100 basepairs apart. In certain embodiments ofthe invention, the single nucleotide polymorphisms in each tandem singlenucleotide polymorphism are each at most about 50 basepairs apart.

In certain embodiments of the invention, at least one tandem singlenucleotide polymorphism is located on the p arm of chromosome 21. Incertain embodiments of the invention, at least one tandem singlenucleotide polymorphism is located on the q arm of chromosome 21.

In certain embodiments of the invention, the chromosomal abnormality ischromosomal aneuploidy. In certain embodiments of the invention, thechromosomal abnormality is trisomy 13, 18 or 21. In certain embodimentsof the invention, the chromosomal abnormality is trisomy 21.

In certain embodiments of the invention, the chromosomal abnormality isan insertion mutation (e.g., a large insertion (≧3 megabasepair) orsmall insertion (<3 megabasepair). In certain embodiments of theinvention, the chromosomal abnormality is a deletion mutation (e.g., alarge deletion (≧3 megabasepair) or small deletion (<3 megabasepair)).The deleted region could include a deleted gene.

In certain embodiments of the invention, the methods can be used todetect copy number polymorphisms and/or copy number variants in thegenome. In certain embodiments of the invention, the methods can be usedto detect chromosome 22q11 deletion syndrome, which is associated withcardiac defects.

Chromosomal abnormalities include deletions associated with geneticsyndromes and disorders such as the 22q11 deletion syndrome onchromosome 22, which is associated with cardiac defects. Other examplesof chromosomal abnormalities include the 11q deletion syndrome onchromosome 11 and 8p deletion syndrome on chromosome 8, both of whichare also associated with cardiac defects.

In certain embodiments of the invention, the fetus is a male fetus. Incertain embodiments of the invention, the fetus is a female fetus. Incertain embodiments of the invention, the fetus is a mammal. In certainembodiments of the invention, the fetus is a human. In certainembodiments of the invention, the fetus is a non-human mammal. Incertain embodiments of the invention, the fetus has been determined tobe at an elevated risk for having a chromosomal abnormality.

In certain embodiments of the invention, the method further comprisesusing tandem single nucleotide polymorphisms to compare paternal DNA tothe fetal and/or maternal DNA.

In certain embodiments of the invention, the fetal DNA is subjected toan enrichment step. In certain embodiments of the invention, the fetalDNA is not subjected to an enrichment step.

Certain embodiments of the present invention provide a method foridentifying chromosomes, comprising comparing tandem single nucleotidepolymorphisms on the chromosomes so as to identify the chromosomes.Thus, the methods of the present invention are not limited tomaternal-fetal analysis, but can also be applied to other situations,e.g., forensic analysis of blood samples.

In certain embodiments of the invention, the methods further comprises,prior to the comparison step, determining a set of tandem singlenucleotide polymorphisms for a specific chromosome.

Certain embodiments of the present invention provide a system comprisingpackaging material and primers that specifically hybridize to each ofthe single nucleotide polymorphisms of at least one of the tandem singlenucleotide polymorphisms identified herein.

Certain embodiments of the present invention provide a system comprisingpackaging material and primers that specifically hybridize flankingsequences of at least one of the tandem single nucleotide polymorphismsof the invention.

Certain embodiments of the present invention provide a system comprisingpackaging material and at least one oligonucleotide that specificallyhybridizes to at least one of the tandem single nucleotide polymorphismsof the invention.

Certain embodiments of the present invention provide the use ofhigh-fidelity PCR (HiFi-PCR) to amplify SNPs or tandem SNPs for thepurpose of, e.g., determining chromosomal abnormalities.

Certain embodiments of the present invention provide the use of HiFi-PCRto amplify nucleic acids, e.g., DNA, isolated, e.g., from a maternalbiological sample to analyze fetal DNA for chromosomal abnormalities.

In certain embodiments, HiFi-PCR is used to detect aneuploidy and large(≧3 megabasepairs) or small (<3 megabasepairs) deletions and/orinsertions.

In certain embodiments, the maternal biological sample is serum, urine,sweat, cells, or cell free DNA.

Certain embodiments of the present invention provide an isolated nucleicacid sequence comprising at least one of SEQ ID NOs 1-357.

Certain embodiments of the present invention provide an isolated nucleicacid sequence of the invention (e.g., a nucleic acid sequence comprisinga tandem SNP or a primer; e.g., at least one of SEQ ID NOs 1-357) foruse in medical treatment or diagnosis.

In certain embodiments, the nucleic acid sequences may be, e.g.,isolated nucleic acid sequences and may be, e.g., about 1000 or fewer,e.g., about 900 or fewer, e.g., about 800 or fewer, e.g., about 700 orfewer, e.g., about 600 or fewer, e.g., about 500 or fewer, e.g., about400 or fewer, e.g., about 300 or fewer, e.g., about 250 or fewer, e.g.,about 200 or fewer, e.g., about 150 or fewer, e.g., about 100 or fewer,or e.g., about 50 or fewer nucleic acids in length.

Thus, short haplotypes are used to detect fetal chromosomalabnormalities in maternal serum, e.g., for the most common of thesedefects, trisomy 21. To demonstrate this method, tandem SNPs forchromosome 21 are identified, heterozygosity of the tandem SNPsdetermined, the ability to detect fetal DNA from maternal serumdemonstrated, and the ability to detect fetal chromosomal abnormalitiesin maternal serum demonstrated. 118 tandem SNPs have already beenidentified. These tandem SNPs are useful in the diagnosis of chromosomalabnormalities, for example, of trisomy 21. Thus, certain embodiments ofthe invention provide the specific tandem SNPs, or combinations thereof,as well as their use in diagnostic and therapeutic applications.

The output of these experiments, e.g., assays based on a set of tandemSNPs for chromosome 21, can be used in the clinic as an alternative toinvasive diagnostic tests like amniocentesis and CVS, using, e.g., CDCEor other techniques capable of detecting the tandem SNPs. Thesediagnostics are sensitive and specific. The tandem SNP assay isparticularly suited for fetal DNA analysis because fetal DNA present inmaternal serum is generally present as short fragments (e.g., an averageof 300 basepairs or fewer).

Thus, certain embodiments of the present invention are directed to eachof these tandem SNPs individually, and certain embodiments are directedto combinations of any and/or all of the tandem SNPs. Certainembodiments of the invention are directed to methods of using the tandemSNPs for diagnosing chromosomal abnormalities. Certain embodiments ofthe invention are directed to compilations of the tandem SNPs (e.g.,reference tables) that are useful for diagnosing chromosomalabnormalities. Certain embodiments of the invention are also directed toprimers for each of these tandem SNPs individually, and certainembodiments are directed to combinations of primers for any and/or allof the tandem SNPs. Certain embodiments of the invention provideisolated nucleic acid sequences that comprise at least one of the tandemSNPs and compositions that comprise the isolated nucleic acid sequences.

Prenatal Screening

An increasing number of fetal medical conditions can be successfullymanaged during the neonatal period if an early diagnosis is made. Avariety of prenatal screening tools are available for chromosomal andbirth defects. The two most commonly utilized non-invasive tools areultrasound and measurements of maternal serum markers. Both of these“tests” have inadequate sensitivity and specificity for screening themost common of the defects, Down Syndrome (trisomy 21).

An ultrasound screening called the nuchal translucency test is becomingmore common. However, this test has an overall sensitivity of 77% fortrisomy 21 with a false positive rate of 6% (Malone et al., ObstetGynecol, 2003. 102(5 Pt 1): p. 1066-79). The most advanced serum markertest is the “quad” screen, which measures the levels ofalpha-fetoprotein (AFP), human chorionic gonadotropin (hCG),unconjugated estriol (E3), and inhibin-A. The biological reason forthese markers to be elevated or reduced in a percentage of motherscarrying children with trisomy 21 is not understood. Further, the testis only capable of assigning risk categories (i.e., 1 in 250, 1 in 100,1 in 10), and not in making specific diagnoses. The quad screen isassociated with a false positive rate of 7% and a sensitivity of lessthan 80%, rates which do not approach those achieved by invasiveprenatal diagnostic tests (Wald et al., Lancet, 2003. 361(9360): p.835-6).

Because of the inadequate sensitivity and specificity of currentlyavailable non-invasive tools, amniocentesis and chorionic villussampling (CVS), both invasive procedures, remain the standard for thedefinitive detection of fetal chromosomal abnormalities. Both of theseprocedures carry a 0.5%-1% fetal loss rate, which translate into thedeath of thousands of normal fetuses annually. To solve this problem andmeet the overwhelming need for an accurate non-invasive test, severalstrategies have been previously proposed by other investigators.However, those studies have been limited by their ability to detect anddifferentiate fetal DNA from maternal DNA.

A PCR-based approach for detecting aneuploidy relies on a method calledquantitative fluorescent polymerase chain reaction (QF-PCR) of shorttandem repeats (STRs). However, polymerase errors are frequently made inthe repeat sequences, generating a high background “noise” for each STRassay. These PCR errors (stutters) make peak area measurements difficultand thus the detection and quantification of low frequency fetal DNA inmaternal serum not possible (Dhallan et al., JAMA, 2004. 291(9): p.1114-9).

In 1994, a technology called constant denaturant capillaryelectrophoresis (CDCE) combined with high-fidelity PCR (HiFi-PCR) wasdeveloped to allow researchers to detect and quantify low frequencysomatic mutations present in heterogeneous cell populations (Khrapko etal., Nucleic Acids Res, 1994. 22(3): p. 364-9). Compared to other DNAseparation methods, CDCE permits the highest resolution separation ofDNA sequences differing by even a single base pair. The separation isbased on differences in the melting temperature and the resultingelectrophoretic mobility differences as the DNA molecules migratethrough a linear polyacrylamide matrix under partially denaturingconditions (Khrapko et al., 1994). CDCE coupled with HiFi-PCR has beendemonstrated to detect mutations in about 100 bp sequences with asensitivity of at least 2×10⁻⁶ in human cells and tissues (Li-Sucholeikiet al., Nucleic Acids Res, 2000. 28(9): p. E44). As described herein,this technology can be applied to single nucleotide polymorphisms(SNPs), natural single basepair variations present in the genome, toseparate alleles. CDCE is used in the present invention to screen tandemSNPs to increase the informativeness (or heterozygosity) of each CDCEassay by increasing the number of possible alleles (or haplotypes)available. Through the use of tandem SNPs, a highly specific andsensitive assay for detecting fetal chromosomal abnormalities by simplycomparing maternal serum to maternal buccal swabs has been created.

High-Fidelity PCR is an amplification method resulting in an error rate(in per basepair doubling) equal to or better than standard PCR. Forexample, Taq polymerase has an error rate of about 10−⁴ per basepairdoubling. As an example, Pyrococcus furiosus (Pfu) is a high-fidelitypolymerase. The published error rate for Pfu is 1.3×10⁻⁶ per basepairdoubling (Cline et al, Nucleic Acids Res. 1996 Sep. 15; 24(18):3546-3551).

Methods for improving PCR fidelity include, among others: A) using ahigh-fidelity polymerase enzyme; and B) the addition of chemicalreagents (e.g., betaine) that can lower temperatures required during thePCR process. The prolonged heating of DNA and nucleotides during PCR canlead to damaged products, such as deaminated cytosines (uracils) andthus lead to misincorporation errors and miscopying errors during PCR(Andre, Kim, Khrapko, Thilly. Genome Res. 1997 7: 843-852. Zheng,Khrapko, Coller, Thilly, Copeland. Mutat Res. 2006 Jul. 25;599(1-2):11-20). Examples of high-fidelity enzymes include Pfu and itsderivations, or other enzymes with similar proofreading 3′→5′exonucleases.

In certain embodiments of the invention, amplification, e.g., HiFi-PCR,is performed with primers being in molar excess (e.g., 10¹² copies/μl ofprimer vs 10⁶ or less of the template) so that it is more likely thatprimers will anneal with template DNA than with each other (see, e.g.,Li-Sucholeiki X C, Thilly W G. Nucleic Acids Res. 2000 May 1; 28(9):E44;Thompson J R, Marcelino L, Polz M. Nucleic Acids Res. 2002 May 1; 30(9):2083-2088.). This can significantly reduce the creation ofheteroduplexes.

A “single nucleotide polymorphism (SNP)” is a single basepair variationin a nucleic acid sequence. A “tandem SNP” is a pair of SNPs that arelocated in a nucleic acid sequence, e.g. on a chromosome, in a mannerthat allows for the detection of both of the SNPs. The distance betweenSNPs generally is about 250 basepairs or fewer, e.g., about 200basepairs or fewer, e.g., about 150 basepairs or fewer, e.g., about 100basepairs or fewer, e.g., about 50 basepairs or fewer. The tandem SNPscan be detected by a variety of means that are capable of detecting thetandem SNPs. In one embodiment of the invention, constant denaturantcapillary electrophoresis (CDCE) can be combined with high-fidelity PCR(HiFi-PCR) to detect the tandem SNP. In another embodiment,hybridization on a microarray is used. In another embodiment,high-fidelity PCR is used and another method capable of detecting SNPspresent at low frequencies is used (e.g., denaturing HPLC, denaturingcapillary electrophoresis, cycling temperature capillaryelectrophoresis, allele-specific PCRs, quantitative real time PCRapproaches such as TaqMan® PCR system, polony sequencing approaches,microarray approaches, and mass spectrometry). In another embodiment,high-throughput sequencing approaches, e.g., at a single molecule level,are used.

The term “nucleic acid” refers to deoxyribonucleotides orribonucleotides and polymers thereof in either single- ordouble-stranded form, made of monomers (nucleotides) containing a sugar,phosphate and a base that is either a purine or pyrimidine. Unlessspecifically limited, the term encompasses nucleic acids containingknown analogs of natural nucleotides that have similar bindingproperties as the reference nucleic acid and are metabolized in a mannersimilar to naturally occurring nucleotides. Unless otherwise indicated,a particular nucleic acid sequence also encompasses conservativelymodified variants thereof (e.g., degenerate codon substitutions) andcomplementary sequences, as well as the sequence explicitly indicated.Specifically, degenerate codon substitutions may be achieved bygenerating sequences in which the third position of one or more selected(or all) codons is substituted with mixed-base and/or deoxyinosineresidues.

The term “nucleotide sequence” refers to a polymer of DNA or RNA whichcan be single-stranded or double-stranded, optionally containingsynthetic, non-natural or altered nucleotide bases capable ofincorporation into DNA or RNA polymers. The terms “nucleic acid,”“nucleic acid molecule,” or “polynucleotide” are used interchangeably.

Certain embodiments of the invention encompass isolated or substantiallypurified nucleic acid compositions. In the context of the presentinvention, an “isolated” or “purified” DNA molecule or RNA molecule is aDNA molecule or RNA molecule that exists apart from its nativeenvironment and is therefore not a product of nature. An isolated DNAmolecule or RNA molecule may exist in a purified form or may exist in anon-native environment such as, for example, a transgenic host cell. Forexample, an “isolated” or “purified” nucleic acid molecule issubstantially free of other cellular material or culture medium whenproduced by recombinant techniques, or substantially free of chemicalprecursors or other chemicals when chemically synthesized. In oneembodiment, an “isolated” nucleic acid is free of sequences thatnaturally flank the nucleic acid (i.e., sequences located at the 5′ and3′ ends of the nucleic acid) in the genomic DNA of the organism fromwhich the nucleic acid is derived.

The following terms are used to describe the sequence relationshipsbetween two or more nucleic acids or polynucleotides: (a) “referencesequence,” (b) “comparison window,” (c) “sequence identity,” (d)“percentage of sequence identity,” and (e) “substantial identity.”

(a) As used herein, “reference sequence” is a defined sequence used as abasis for sequence comparison. A reference sequence may be a subset orthe entirety of a specified sequence; for example, as a segment of afull-length cDNA or gene sequence, or the complete cDNA or genesequence.

(b) As used herein, “comparison window” makes reference to a contiguousand specified segment of a polynucleotide sequence, wherein thepolynucleotide sequence in the comparison window may comprise additionsor deletions (i.e., gaps) compared to the reference sequence (which doesnot comprise additions or deletions) for optimal alignment of the twosequences. Generally, the comparison window is at least 20 contiguousnucleotides in length, and optionally can be 30, 40, 50, 100, or longer.Those of skill in the art understand that to avoid a high similarity toa reference sequence due to inclusion of gaps in the polynucleotidesequence a gap penalty is typically introduced and is subtracted fromthe number of matches.

Methods of alignment of sequences for comparison are well-known in theart. Thus, the determination of percent identity between any twosequences can be accomplished using a mathematical algorithm.Non-limiting examples of such mathematical algorithms are the algorithmof Myers and Miller (Myers and Miller, CABIOS, 4, 11 (1988)); the localhomology algorithm of Smith et al. (Smith et al., Adv. Appl. Math., 2,482 (1981)); the homology alignment algorithm of Needleman and Wunsch(Needleman and Wunsch, J M B, 48, 443 (1970)); thesearch-for-similarity-method of Pearson and Lipman (Pearson and Lipman,Proc. Natl. Acad. Sci. USA, 85, 2444 (1988)); the algorithm of Karlinand Altschul (Karlin and Altschul, Proc. Natl. Acad. Sci. USA, 87, 2264(1990)), modified as in Karlin and Altschul (Karlin and Altschul, Proc.Natl. Acad. Sci. USA 90, 5873 (1993)).

Computer implementations of these mathematical algorithms can beutilized for comparison of sequences to determine sequence identity.Such implementations include, but are not limited to: CLUSTAL in thePC/Gene program (available from Intelligenetics, Mountain View, Calif.);the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, andTFASTA in the Wisconsin Genetics Software Package, Version 8 (availablefrom Genetics Computer Group (GCG), 575 Science Drive, Madison, Wis.,USA). Alignments using these programs can be performed using the defaultparameters. The CLUSTAL program is well described by Higgins et al.(Higgins et al., CABIOS, 5, 151 (1989)); Corpet et al. (Corpet et al.,Nucl. Acids Res., 16, 10881 (1988)); Huang et al. (Huang et al., CABIOS,8, 155 (1992)); and Pearson et al. (Pearson et al., Meth. Mol. Biol.,24, 307 (1994)). The ALIGN program is based on the algorithm of Myersand Miller, supra. The BLAST programs of Altschul et al. (Altschul etal., JMB, 215, 403 (1990)) are based on the algorithm of Karlin andAltschul supra.

Software for performing BLAST analyses is publicly available through theNational Center for Biotechnology Information. This algorithm involvesfirst identifying high scoring sequence pairs (HSPs) by identifyingshort words of length W in the query sequence, which either match orsatisfy some positive-valued threshold score T when aligned with a wordof the same length in a database sequence. T is referred to as theneighborhood word score threshold. These initial neighborhood word hitsact as seeds for initiating searches to find longer HSPs containingthem. The word hits are then extended in both directions along eachsequence for as far as the cumulative alignment score can be increased.Cumulative scores are calculated using, for nucleotide sequences, theparameters M (reward score for a pair of matching residues; always >0)and N (penalty score for mismatching residues; always <0). For aminoacid sequences, a scoring matrix is used to calculate the cumulativescore. Extension of the word hits in each direction are halted when thecumulative alignment score falls off by the quantity X from its maximumachieved value, the cumulative score goes to zero or below due to theaccumulation of one or more negative-scoring residue alignments, or theend of either sequence is reached.

In addition to calculating percent sequence identity, the BLASTalgorithm also performs a statistical analysis of the similarity betweentwo sequences. One measure of similarity provided by the BLAST algorithmis the smallest sum probability (P(N)), which provides an indication ofthe probability by which a match between two nucleotide or amino acidsequences would occur by chance. For example, a test nucleic acidsequence is considered similar to a reference sequence if the smallestsum probability in a comparison of the test nucleic acid sequence to thereference nucleic acid sequence is less than about 0.1, less than about0.01, or even less than about 0.001.

To obtain gapped alignments for comparison purposes, Gapped BLAST (inBLAST 2.0) can be utilized. Alternatively, PSI-BLAST (in BLAST 2.0) canbe used to perform an iterated search that detects distant relationshipsbetween molecules. When utilizing BLAST, Gapped BLAST, PSI-BLAST, thedefault parameters of the respective programs (e.g., BLASTN fornucleotide sequences, BLASTX for proteins) can be used. The BLASTNprogram (for nucleotide sequences) uses as defaults a wordlength (W) of11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and acomparison of both strands. For amino acid sequences, the BLASTP programuses as defaults a wordlength (W) of 3, an expectation (E) of 10, andthe BLOSUM62 scoring matrix. Alignment may also be performed manually byinspection.

For purposes of the present invention, comparison of nucleotidesequences for determination of percent sequence identity to the promotersequences disclosed herein may be made using the BlastN program (version1.4.7 or later) with its default parameters or any equivalent program.By “equivalent program” is intended any sequence comparison programthat, for any two sequences in question, generates an alignment havingidentical nucleotide or amino acid residue matches and an identicalpercent sequence identity when compared to the corresponding alignmentgenerated by the program.

(c) As used herein, “sequence identity” or “identity” in the context oftwo nucleic acid or polypeptide sequences makes reference to a specifiedpercentage of residues in the two sequences that are the same whenaligned for maximum correspondence over a specified comparison window,as measured by sequence comparison algorithms or by visual inspection.When percentage of sequence identity is used in reference to proteins itis recognized that residue positions which are not identical oftendiffer by conservative amino acid substitutions, where amino acidresidues are substituted for other amino acid residues with similarchemical properties (e.g., charge or hydrophobicity) and therefore donot change the functional properties of the molecule. When sequencesdiffer in conservative substitutions, the percent sequence identity maybe adjusted upwards to correct for the conservative nature of thesubstitution. Sequences that differ by such conservative substitutionsare said to have “sequence similarity” or “similarity.” Means for makingthis adjustment are well known to those of skill in the art. Typicallythis involves scoring a conservative substitution as a partial ratherthan a full mismatch, thereby increasing the percentage sequenceidentity. Thus, for example, where an identical amino acid is given ascore of 1 and a non-conservative substitution is given a score of zero,a conservative substitution is given a score between zero and 1. Thescoring of conservative substitutions is calculated, e.g., asimplemented in the program PC/GENE (Intelligenetics, Mountain View,Calif.).

(d) As used herein, “percentage of sequence identity” means the valuedetermined by comparing two optimally aligned sequences over acomparison window, wherein the portion of the polynucleotide sequence inthe comparison window may comprise additions or deletions (i.e., gaps)as compared to the reference sequence (which does not comprise additionsor deletions) for optimal alignment of the two sequences. The percentageis calculated by determining the number of positions at which theidentical nucleic acid base or amino acid residue occurs in bothsequences to yield the number of matched positions, dividing the numberof matched positions by the total number of positions in the window ofcomparison, and multiplying the result by 100 to yield the percentage ofsequence identity.

(e)(i) The term “substantial identity” of polynucleotide sequences meansthat a polynucleotide comprises a sequence that has at least 70%, 71%,72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, or 94%, or even at least 95%,96%, 97%, 98%, or 99% sequence identity, compared to a referencesequence using one of the alignment programs described using standardparameters. One of skill in the art will recognize that these values canbe appropriately adjusted to determine corresponding identity ofproteins encoded by two nucleotide sequences by taking into accountcodon degeneracy, amino acid similarity, reading frame positioning, andthe like. Substantial identity of amino acid sequences for thesepurposes normally means sequence identity of at least 70%, 80%, 90%, oreven at least 95%.

Another indication that nucleotide sequences are substantially identicalis if two molecules hybridize to each other under stringent conditions.Generally, stringent conditions are selected to be about 5° C. lowerthan the thermal melting point (T_(m)) for the specific sequence at adefined ionic strength and pH. However, stringent conditions encompasstemperatures in the range of about 1° C. to about 20° C., depending uponthe desired degree of stringency as otherwise qualified herein. Nucleicacids that do not hybridize to each other under stringent conditions arestill substantially identical if the polypeptides they encode aresubstantially identical. This may occur, e.g., when a copy of a nucleicacid is created using the maximum codon degeneracy permitted by thegenetic code. One indication that two nucleic acid sequences aresubstantially identical is when the polypeptide encoded by the firstnucleic acid is immunologically cross reactive with the polypeptideencoded by the second nucleic acid.

(e)(ii) The term “substantial identity” in the context of a peptideindicates that a peptide comprises a sequence with at least 70%, 71%,72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, or 94%, or even 95%, 96%, 97%,98% or 99%, sequence identity to the reference sequence over a specifiedcomparison window. In certain embodiments, optimal alignment isconducted using the homology alignment algorithm of Needleman and Wunsch(Needleman and Wunsch, J M B, 48, 443 (1970)). An indication that twopeptide sequences are substantially identical is that one peptide isimmunologically reactive with antibodies raised against the secondpeptide. Thus, a peptide is substantially identical to a second peptide,for example, where the two peptides differ only by a conservativesubstitution. Thus, certain embodiments of the invention provide nucleicacid molecules that are substantially identical to the nucleic acidmolecules described herein.

For sequence comparison, typically one sequence acts as a referencesequence to which test sequences are compared. When using a sequencecomparison algorithm, test and reference sequences are input into acomputer, subsequence coordinates are designated if necessary, andsequence algorithm program parameters are designated. The sequencecomparison algorithm then calculates the percent sequence identity forthe test sequence(s) relative to the reference sequence, based on thedesignated program parameters.

As noted above, another indication that two nucleic acid sequences aresubstantially identical is that the two molecules hybridize to eachother under stringent conditions. The phrase “hybridizing specificallyto” refers to the binding, duplexing, or hybridizing of a molecule onlyto a particular nucleotide sequence under stringent conditions when thatsequence is present in a complex mixture (e.g., total cellular) DNA orRNA. “Bind(s) substantially” refers to complementary hybridizationbetween a probe nucleic acid and a target nucleic acid and embracesminor mismatches that can be accommodated by reducing the stringency ofthe hybridization media to achieve the desired detection of the targetnucleic acid sequence.

“Stringent hybridization conditions” and “stringent hybridization washconditions” in the context of nucleic acid hybridization experimentssuch as Southern and Northern hybridizations are sequence dependent, andare different under different environmental parameters. Longer sequenceshybridize specifically at higher temperatures. The thermal melting point(Tm) is the temperature (under defined ionic strength and pH) at which50% of the target sequence hybridizes to a perfectly matched probe.Specificity is typically the function of post-hybridization washes, thecritical factors being the ionic strength and temperature of the finalwash solution. For DNA-DNA hybrids, the T_(m) can be approximated fromthe equation of Meinkoth and Wahl (1984); T_(m) 81.5° C.+16.6 (logM)+0.41 (% GC)−0.61 (% form)−500/L; where M is the molarity ofmonovalent cations, % GC is the percentage of guanosine and cytosinenucleotides in the DNA, % form is the percentage of formamide in thehybridization solution, and L is the length of the hybrid in base pairs.T_(m) is reduced by about 1° C. for each 1% of mismatching; thus, T_(m),hybridization, and/or wash conditions can be adjusted to hybridize tosequences of the desired identity. For example, if sequences with >90%identity are sought, the T_(m) can be decreased 10° C. Generally,stringent conditions are selected to be about 5° C. lower than the T_(m)for the specific sequence and its complement at a defined ionic strengthand pH. However, severely stringent conditions can utilize ahybridization and/or wash at 1, 2, 3, or 4° C. lower than the T_(m);moderately stringent conditions can utilize a hybridization and/or washat 6, 7, 8, 9, or 10° C. lower than the T_(m); low stringency conditionscan utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C.lower than the T_(m). Using the equation, hybridization and washcompositions, and desired temperature, those of ordinary skill willunderstand that variations in the stringency of hybridization and/orwash solutions are inherently described. If the desired degree ofmismatching results in a temperature of less than 45° C. (aqueoussolution) or 32° C. (formamide solution), the SSC concentration isincreased so that a higher temperature can be used. Generally, highlystringent hybridization and wash conditions are selected to be about 5°C. lower than the T_(m) for the specific sequence at a defined ionicstrength and pH.

An example of highly stringent wash conditions is 0.15 M NaCl at 72° C.for about 15 minutes. An example of stringent wash conditions is a0.2×SSC wash at 65° C. for 15 minutes. Often, a high stringency wash ispreceded by a low stringency wash to remove background probe signal. Anexample medium stringency wash for a duplex of, e.g., more than 100nucleotides, is 1×SSC at 45° C. for 15 minutes. For short nucleotidesequences (e.g., about 10 to 50 nucleotides), stringent conditionstypically involve salt concentrations of less than about 1.5 M, lessthan about 0.01 to 1.0 M, Na ion concentration (or other salts) at pH7.0 to 8.3, and the temperature is typically at least about 30° C. andat least about 60° C. for long probes (e.g., >50 nucleotides). Stringentconditions may also be achieved with the addition of destabilizingagents such as formamide. In general, a signal to noise ratio of 2× (orhigher) than that observed for an unrelated probe in the particularhybridization assay indicates detection of a specific hybridization.Nucleic acids that do not hybridize to each other under stringentconditions are still substantially identical if the proteins—that theyencode are substantially identical. This occurs, e.g., when a copy of anucleic acid is created using the maximum codon degeneracy permitted bythe genetic code.

Very stringent conditions are selected to be equal to the T_(m) for aparticular probe. An example of stringent conditions for hybridizationof complementary nucleic acids that have more than 100 complementaryresidues on a filter in a Southern or Northern blot is 50% formamide,e.g., hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and awash in 0.1×SSC at 60 to 65° C. Exemplary low stringency conditionsinclude hybridization with a buffer solution of 30 to 35% formamide, 1 MNaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C.Exemplary moderate stringency conditions include hybridization in 40 to45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSCat 55 to 60° C.

In addition to the chemical optimization of stringency conditions,analytical models and algorithms can be applied to hybridizationdata-sets (e.g. microarray data) to improve stringency.

The term “treatment” or “treating,” to the extent it relates to adisease or condition includes preventing the disease or condition fromoccurring, inhibiting the disease or condition, eliminating the diseaseor condition, and/or relieving one or more symptoms of the disease orcondition.

The invention will now be illustrated by the following non-limitingExamples.

Example 1 Tandem SNPs for Chromosome 21

96 allelic markers on chromosome 21 are selected by examining tandemSNPs. These tandem SNPs will cover both q and p arms of the chromosome.Using heterozygosity data available through dbSNP, DCC Genotype Databaseand through the HapMap Project, SNPs that appear to be promising forhigh heterozygosity (≧25%) are selected. Because all four possibilitiesmay not exist in nature due to haplotype blocks in regions of lowrecombination, those that suggest less than three haplotypes arescreened out. FIG. 1 depicts an example of tandem SNPs (SNP 1=rs2839416,average estimated heterozygosity 0.444 and SNP2=rs2839417, averageestimated heterozygosity 0.414).

Target sequences covering tandem SNPs are designed using Vector NTI andWinMelt software. As an example, the melting map of a CDCE targetcovering two tandem SNPs (dbSNP rs2839416 and rs2839417) on chromosome21 was calculated using WinMelt according to the algorithm of Lerman andSilverstein (Lerman et al., Methods Enzymol, 1987. 155: p. 482-501) andis depicted in FIG. 2.

FIG. 2 depicts a DNA melting map of a CDCE target sequence coveringtandem SNPs. All four haplotypes can be theoretically separatedaccording to DNA melting temperature. The black line indicates haplotype1 (G,A). The yellow line indicates haplotype 2 (T,A). The red lineindicates haplotype 3 (G,G). The green line indicates haplotype 4 (T,G).

HiFi PCR optimization for each target sequence is performed using Pfupolymerase. One of primers flanking the target sequence is ˜20 bases inlength and labeled 5′ with a fluorescein molecule. The other primer isabout 74 bases including a ˜20-base target specific sequence and the54-base clamp sequence. A standard HiFi PCR condition is applied to alltarget sequences, varying only annealing temperatures. These PCRamplicons are subjected to CDCE electrophoretic separation. Theresulting electropherogram are analyzed for yield and purity of the PCRproducts. The purity is evaluated by comparing the peak area of thedesired products to that of the byproducts and nonspecificamplification. Target sequences that can be amplified with a high PCRefficiency (≧45% per cycle) and low levels of byproducts and nonspecificamplification (≧0.1% of the desired products) are immediately besubjected to CDCE optimization. For those target sequences that do nothave acceptable PCR products in the first stage, increasing amounts ofMg⁺² concentrations (up to about 7 mM) in combination with differentannealing temperatures are tested. For the remaining target sequencesthat still do not work, primer positions are changed and the entireoptimization process is repeated.

For CDCE optimization, the relevant haplotypes are created for thetargets. The optimal separation condition for each haplotype shouldprovide the greatest resolution among the observed peaks. Initialoptimization is done around the theoretical melting temperature (T_(m))in a 2° C. temperature range in increments of 0.2° C. which covers(T_(m)−1° C.±a predetermined offset) to (T_(m)+1° C.±a predeterminedoffset).

Electropherogram and peak measurements are transferred to a spreadsheetfor analysis. To ensure the quality of the data, minimum and maximumpeak heights are used. Individual markers are failed if electrophoreticspikes occur. Peak areas are used to calculate allele ratios. A checkfor allelic preferential amplification is performed on all 96 tandemSNPs.

Results

In the fall of 2005, the International HapMap Project publicly releasedgenotypes and frequencies from 270 people of four ethnic populations.Chromosome 21 haplotype data from approximately 40,000 SNPs genotypedacross four populations, including U.S. residents with northern andwestern European ancestry, residents of Ibadan, Nigeria, of Tokyo,Japan, and of Beijing, China, were downloaded (2005-10-24: HapMap PublicRelease #19) and converted to the + orientation. Tandem SNP candidatesfell within 100 basepairs from each other and at least three haplotypesexisted in all four ethnic populations. CDCE target sequences andprimers are designed for the tandem SNPs identified through the HapMapProject. The neighboring sequences for each of the tandem SNPs areimported into a software program, e.g., Sequencher (Gene Codes, AnnArbor, Mich.) and/or Vector NTI (Invitrogen, Carlsbad, Calif.) forsequence alignment and primer design, and into Winmelt (Medprobe, Oslo,Norway) or Poland software (available on the world wide web atbiophys.uniduesseldorf.de/local/POLAND/poland.html) where the algorithmfor computing DNA melting temperatures given the Gotoh-Tagashira valuesfor the enthalpy of melting DNA sequences are used to calculate meltingtemperatures of target sequences. CDCE candidates generally have a highmelting region adjacent to a low melting region, lie in a low meltingregion, melting temperatures of the low melting region fall below 80°C., and no “valleys” occur between the high melting region and the lowmelting region.

All of the 40,000 genotypes on chromosome 21 have been analyzed fortandem SNP/CDCE marker suitability. 118 tandem SNPs/CDCE targets meetingour requirements have been identified (see Table 1 for the first 42identified and Table 2 for all 118).

Primer sequences for these 118 tandem SNP/CDCE targets have beendesigned. These will be optimized as described herein using HiFi PCR andCDCE. These optimizations are described herein and include the creationof relevant haplotypes for all targets, a check for allelic preferentialamplification during HiFi PCR, and obtaining the greatest resolutionamong peaks during CDCE. Haplotypes may be separated as homoduplexpeaks. However, if certain targets cannot be separated out ashomoduplexes, maternal DNA can be separated from fetal DNA asheteroduplexes.

TABLE 1 Tandem SNP #/Observed dbSNP Chromosome   haplotypes NameChromosome Position bp dif  1

A/C Chr21

CC/CT/AC

C/T Chr21

 2

A/C Chr21

AA/AS/CG/CA

A/G Chr21

 3 rs2822785 A/G Chr21 14676399 65 AG/GG/AA/GA rs2822786 A/G Chr2114876464  4 rs2822786 A/G Chr21 14876464 67 GC/AC/GT rs2822787 C/T Chr2114876531  5

A/G Chr21 14948471 97 AA/GT/GA

A/T Chr21

 6

C/T Chr21

CA/CG/TG

A/G Chr21

 7

A/G Chr21

72 At/ 

C/T Chr21

 8

A/G Chr21

GG/ 

G/T Chr21

 9

C/T Chr21

CT/CC/TT

C/T Chr21

10

C/T Chr21

TC/CC/TT

C/T Chr21

11

C/T Chr21

TA/CA/TG

A/G Chr21

12

A/G Chr21

78 GG/AC/GC

C/G Chr21

13

A/G Chr21

AA/GG/AG rs2823349 A/G Chr21 15833601 14 rs2823502 A/C Chr21 16124651 32AT/AC/CT/CC rs2823503 C/T Chr21 16124683 15 rs960391 C/T Chr21 1703486429 CC/CA/TC/TA rs13049140 A/C Chr21 17034893 16 rs2824078 C/T Chr2117134418 30 CA/TA/TG

A/G Chr21 17134448 17 rs1999289 C/T Chr21 17696177 92 CT/CC/TC rs208897C/T Chr21 17896269 18

A/G Chr21 17744045

GG/GA/AA/AG

A/G Chr21 17744144 19

A/G Chr21

GG/AA/AG/GA

A/G Chr21

20

C/G Chr21

GG/CG/CC/GC

C/G Chr21

21

A/G Chr21

GT/GC/AT/AC

C/T Chr21

22

A/G Chr21

79 GG/ 

G/T Chr21

23

A/G Chr21

AA/GT/GA/AT

A/T Chr21

24

A/T Chr21

AC/TA/TC/AA

A/C Chr21

25

C/T Chr21

CT/TC/CC/TT

C/T Chr21

26

G/T Chr21

TT/GC/GT rs2825926 C/T Chr21 20272639 27 rs377685 A/G Chr21 20272988 33GT/AT/GC/AC rs420778 C/T Chr21 20273021 28 rs2826058 A/C Chr21 20464969

AG/GT/CG

G/T Chr21

29

G/T Chr21

CT/CC/TT

C/T Chr21

30

C/T Chr21

CC/TC/TT

C/T Chr21

31

C/T Chr21

CA/TA/CG/TG

A/G Chr21

32

C/T Chr21

TG/CA/CG/GA

A/G Chr21

33

A/G Chr21

GA/AA/GG

A/G Chr21

34

C/G Chr21

GA/GG/CA

A/G Chr21

35

C/G Chr21

CG/GG/GC/CC

C/G Chr21

36

C/G Chr21

GC/GT/CC/CT

C/T Chr21

37 rs1735934 A/G Chr21 21995535 78 AC/GC/GT rs2826958 C/T Chr21 2199563338 rs994676 A/G Chr21 22043945 34 AC/GT/AT/GC rs2826982 C/T Chr2122043979 39

A/G Chr21

AA/GC/AC

A/C Chr21

40

A/ 

Chr21

AA/GA/ 

A/ 

Chr21

41 rs244260 A/G Chr21 23311737 88 AT/GT/AC/GC

C/T Chr21

42

A/C Chr21

47 CG/CC/AG/AC

C/G Chr21

indicates data missing or illegible when filed

Example 2 Determining Heterozygosity of the Tandem SNPs

As a complement to Example 1, genomic DNA samples from 300 anonymoussubjects have been obtained from healthy young adults who are less than35 years old. The samples are anonymous as the only data obtained werethe geographic location of the Red Cross blood donor center, donorgender, and whether or not the donor was 35 and under. These sampleswere spot-checked to look for the haplotypes seen in the HapMap project.

Example 3 Detecting Fetal DNA from Maternal Serum

A cohort of patients who have been confirmed to have trisomy 21 bytraditional karyotype analysis are examined. Tandem SNPs are used todemonstrate detection of trisomy in patients. DNA from 20 patients whohave been characterized by traditional karyotype analysis to havetrisomy 21 are analyzed with the tandem SNP panel.

Biological samples, including a buccal (cheek) swab and a blood sampleare collected from a cohort of pregnant women. Maternal buccal swabsamples are compared to maternal serum to demonstrate that a third(paternal) peak is observed in several of the tandem SNP assays.Approximately 20 maternal buccal swab to maternal serum comparisons aremade. To control for experimental artifacts, genomic DNA samples frommaternal buccal swabs are utilized for each target sequence. The buccalsamples are subjected to the process in parallel with the maternal bloodsample. Any artifacts generated by the CDCE/HiFi-PCR procedure(including nonspecific PCR amplification and polymerase-inducedmutations) are revealed as background peaks in the buccal swab samples.

Example 4 Detecting Fetal Chromosomal Abnormalities

A blinded study is performed where the goal is to detect 20 knowntrisomy 21 fetuses by assaying maternal serum from 40 patients(previously determined by amniocentesis or CVS) (see FIG. 3).

FIG. 3 depicts an example of a CDCE electropherogram output with thepeaks at full scale. FIG. 3A depicts a sample from maternal buccal swab.Markers exhibiting two alleles are pursued. A baby with trisomy isexpected to show either three alleles, evident by three peaks in a 1:1:1ratio or two alleles in a 2:1 ratio. FIG. 3B depicts a sample frommaternal serum. Markers exhibiting three alleles are informative.Maternal serum from a woman carrying a baby with trisomy is expected toexhibit three alleles, evident by two equal peaks with a third smallerpeak if the trisomy occurred during meiosis I (75% of T21 cases) orthree alleles with different areas if the trisomy occurred duringmeiosis II (20% of T21 cases) where areas are: peak, x, and peak+2x.FIG. 3C depicts analysis of a sample from maternal serum. Markersexhibiting three alleles are informative. Maternal serum from a womanwith a normal baby with three alleles has three different areas whereareas are: peak, x, and peak+x.

Interpretation of Results

For the case of the minimum heterozygosity, where both SNP1 and SNP2 areheterozygous at their respective loci at a rate of 25%, if 96 tandemSNPs are assayed, an average of 43 markers (44.5%) are expected to beheterozygous (two haplotypes) in the mother. The mother's expectedheterozygosity is calculated using the following formula:

H=1−Σp _(i) ²

for i=1 to k alleles where p_(i)=estimated allele frequency.

The allele frequencies at each SNP loci are expected to be 85% and 15%for the majority and minority alleles, respectively, assumingHardy-Weinberg equilibrium. The desired third haplotype is expected tobe present at an average of 6.4 markers (15%) of per maternal-fetalsample tested. Because most loci have a heterozygosity value greaterthan 25%, for every maternal-fetal sample tested using the panel of 96tandem SNP assays, greater than about 6.4 markers are most informative.Thus, while a panel of 96 tandem SNPs may be used, 6 or 7 of thosetandem SNPs may be informative for any one specific maternal-fetalsample tested, and a ‘positive’ result from any one of those tandem SNPsis informative.

Finally, in order to diagnose a trisomy, a “positive” tandem SNPs shouldbe identified on both the p and the q arm of chromosome 21. Because ofthe comparative nature of the basic approach, the tandem SNP assay ispredicted to have a detection rate of 95% (those that occur duringmaternal meiosis) for trisomy 21. If paternal samples are available,non-disjunctions that occur during paternal meiosis can also bedetected. Thus, detection rates would be higher (about ˜99%) with a 0%false positive rate.

Example 5 Tandem SNPs and Primers

Table 2 provides exemplary tandem SNPs of the invention and primers thatcan be used in the methods of the invention to detect the tandem SNPs.Certain embodiments of the present invention provide primers that can beused to amplify at least one of the SNPs. Certain embodiments of thepresent invention provide nucleic acid sequences that comprise at leastone of the SNPs, e.g., at least one of the tandem SNPs.

TABLE 2 1) Whole sequence 

 rs432114-rs365433 CC/CT/GC/GTAACAAATCTTCATCTTGGAATAGCCTGTGAGAATGCCTAATCATCTACGAATgTTACTTTGGCACCATCTACTGGACAgATTAAATAACAACCAACTCACTGTGGATTAGACCTACTTCTATTTCAG (SEQ ID NO: 1)OLIGO start len tm qc % any ci\Documents and Settings\RamakrishnaMulpuri\Desktop\first 10 primers-redesigned\primer3_www_results_help.cgi-PRIMER_THREE 3′ seq (SEQ ID NOs: 2, 3) LEFT PRIMER 20 20 25.08 45.003.00 2.00 ATAGCCTGTGAGAATGCCTA RIGHT PRIMER 107 20 55.30 45.00 5.00 0.00ATCCACAGTGAGTTGGTTGT SEQUENCE SIZE: 127 INCLUDED REGION SIZE: 127PRODUCT SIZE: 88, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 1.00   1AACAAATCTTCATCTTGGAATAGCCTGTGAGAATGCCTAATCATCTACGAATgTTACTTT      >>>>>>>>>>>>>>>>>>>>  61GGCACCATCTACTGGACAgATTAAATAACAACCAACTCACTGTGGATTAGACCTACTTCT          <<<<<<<<<<<<<<<<<<<< 121 ATTTCAG 2) Whole sequence 

 rs7277033-rs2110153 CC/CT/TC/TT PCR did not workTTCCTGGAAAACAAAAGTATTTCTTTCATAGCCCAGCTAGCAGATAAATCAGCgAGTCAGAATTCTAGCTTTGTTGTAAGGTT (SEQ ID NO: 4)OLIGO start len tm gc % any C:\Documents and Settings\RamakrishnaMulpuri\Destop\first 10 primers-redesigned\primer3_www_results_help.cgi-PRIMER_THREE 3′ (SEQ ID NOs: 5, 6) LEFT PRIMER 2 20 5

TCCTGGAAAACAAAAGTATT RIGHT PRIMER 84 21

4.00

AACCTTACAACAAAGCTAGAA SEQUENCE SIZE: 84 INCLUDED REGION SIZE: 84PRODUCT SIZE: 83, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 2.00   1TTCCTGGAAAACAAAAGTATTTCTTTCATAGCCCAGCTAGCAGATAAATCAGCgAGTCA >>>>>>>>>>>>>>>>>>>> 61 GAATTCTAGCTTTGTTGTAAGGTT <<<<<<<<<<<<<<<<<<<< 3) Whole sequence 

 rs2822654-rs1882882 AA/AG/CA/CGCACTAAGCCTTGGGGATCCAGCTGCTTaAGGACTAAGACCgTATCTAGCTCCTTTTAGTATTTCCACAGCA (SEQ ID NO: 7)OLIGO start len tm gc % any c:\Documents and Settings\RamakrishnaMulpuri\Desktop\first 10 primers-redesigned\primer3_www_results_help.cgi-PRIMER_THREE 3′ seq (SEQ ID NOs: 8, 9) LEFT PRIMER 2 26 50.46 55.00 6.002.00 ACTAAGCCTTGGGGATCCAG RIGHT PRIMER 71 21 54.76 36.10 3.00 0.00TGCTGTGGAAATACTAAAAGG SEQUENCE SIZE: 71 INCLUDED REGION SIZE: 71PRODUCT SIZE: 70, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1CACTAAGCCTGGGGATCCAGCTGCTTaAGGACTAAGACCgTATCTAGCTCCTTTTAGTA >>>>>>>>>>>>>>>>>>>>      <<<<<<<<<<  61 TTTCCACAGCA <<<<<<<<<< 4) Whole sequence 

 rs:368657-rs376635 AA/AG/GA/GGTCCTCCAGAGGTAATCCTGTGATCAGCACTAACaCCACATACCAGCCCTTTCATCAGCTTGTTGGAGAAGCATCTTTACTTCCCgCCAAGCAGTGACCTagataccatctcacaccagttagaatcaggatcattaaaaagtcaagaaaaaacag (SEQ ID NO: 10)OLIGO start len tm gc % any c:\Documents and Settings\RamakrishnaMulpuri\Desktop\first 10 primers-redesigned\primer3_www_results_help.cgi-PRIMER_THREE 3′ seq (SEQ ID NOs: 11, 12) LEFT PRIMER 3 20 55.20 50.005.00 3.00 CTCCAGAGGTAATCCTGTGA RIGHT PRIMER 117 21 55.10

5.00 2.00

SEQUENCE SIZE: 

INCLUDED REGION SIZE: 

PRODUCT SIZE: 115, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 2.00   1TCCTCCAGAGGTAATCCTGTGATCAGCACTAACaCCACATACCAGCCCTTTCATCAGCTT >>>>>>>>>>>>>>>>>>>> 61 GTTGGAGAAGCATCTTTACTTCCCgCCAAGCAGTGACCTagataccatctcacaccagtt             <<<<<<<<<<<<<<<<<<<< 121agaatcaggatcattaaaaagtcaagaaaaaacag 5) Whole sequence 

 rs2822731-rs2822732 AA/AG/GA/GGTCCAAGTATAATCCATGAATCTTGTTTAAATATAGATCAAaTAAACCACTATACCAAAAACATCAAAAGACAACTGGGTAAATTTTTTAAATGACTAGCTATTTGATGTTAAgGAAGTAATGTTACTCTCTTATATACAATTTGAA (SEQ ID NO: 13)OLIGO start len tm gc % any c:\Documents and Settings\RamakrishnaMulpuri\Desktop\first 10 primers-redesigned\primer3_www_results_help.cgi-PRIMER_THREE 3′ seq (SEQ ID NOs: 14, 15) LEFT PRIMER 6 22 50.35 27.276.00 5.00 CTATAATCCATGAATCTTGTTT RIGHT PRIMER 140 23 45.59 22.73 6.001.00 TTCAAATTGTATATAAGAGAGT SEQUENCE SIZE: 146 INCLUDED REGION SIZE: 146PRODUCT SIZE: 141, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 2.00   1TCCAAGTATAATCCATGAATCTTGTTTAAATATAGATCAAaTAAACCACTATACCAAAAA  >>>>>>>>>>>>>>>>>>>>  61CATCAAAAGACAACTGGGTAAATTTTTTAAATGACTAGCTATTTGATGTTAAgGAAGTAA 121TGTTAGTCTCTTATATACAATTTGAA <<<<<<<<<<<<<<<<<<<< 6) Whole sequence 

 rs6516899-rs455221 CC/CT/TC/TTATGGAACCGAAACTTCAAGTAGTTTCATAcGTATCACATTGACAGTTTTCTCTAAGTTTTCTGGTCTTATGACTCGTTGTTTCATTATTAAAACTGTGCCAGTGTATGCATAGGGCTTAGAAATTTTTTAAT (SEQ ID NO: 16)OLIGO start len tm gc % any c:\Documents and Settings\RamakrishnaMulpuri\Desktop\first 10 primers-redesigned\primer3_www_results_help.cgi-PRIMER_THREE 3′ seq (SEQ ID NOs: 17, 18) LEFT PRIMER 1 18 53.87 38.894.00 3.00 ATGGAACCGAAACTTCAA RIGHT PRIMER 81 22

27.27 5.00 1.00 TTAATAATGAAACAACGAGTCA SEQUENCE SIZE: 132INCLUDED REGION SIZE: 132 PRODUCT SIZE: 

, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 

  1ATGGAACCGAAACTTCAAGTAGTTTCATAcGTATCACATTGACAGTTTTCTCTAAGTTTT >>>>>>>>>>>>>>>>>>>> 61 CtGGTCTTATGACTCGTTGTTTCATTATTAAAACTGTGCCAGTGTATGCATAGGGCTTAG   <<<<<<<<<<<<<<<<<<<< 121 AAATTTTTTAAT 7) Whole sequence 

 rs7275381-rs12627144 GA/GG/TA/TGacaggatccttcctgaagacaccaccttggggagggtgaagGataaagaattgatcagaaatcaagggtggtgagatacatgttaaggatgaataaactggccttttaggattcttgctaaaAttagacaatgcagaggcaaccacagagtccaag (SEQ ID NO: 19)OLIGO start len tm gc % any c:\Documents and Settings\RamakrishnaMulpuri\Desktop\first 10 primers-redesigned\primer3_www_results_help.cgi-PRIMER_THREE 3′ seq (SEQ ID NOs: 20, 21) LEFT PRIMER 10 19 55.53 47.374.00 0.00 ttcctgaagacaccacctt RIGHT PRIMER 157 18 54.94 55.56 3.00 2.00cttggactctgtcgttgc SEQUENCE SIZE: 157 INCLUDED REGION SIZE: 157PRODUCT SIZE: 148, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 1.00   1acaggatccttcctgaagacaccaccttggggagggtgaagGataaagaatttgatcaga    >>>>>>>>>>>>>>>>>>>>  61

121 aaaAttagacaatgcagaggcaaccacagagtccaag         <<<<<<<<<<<<<<<<<<<<8) Whole sequence 

 rs1999288-rs208897 CC/CT/TCAATTTCCATTAAATCTTGTTCGTTGCTTTACTGAGGCACTGAAGTTAGGAATGTTcCACTGGTTGACCTGCGGGGCTATCTCTAGGTTATGTTACTCCAGAAAATGAATTGTGTATAAAAGAGGCCTTGGAGGAAGGCGTTTTATTCaCATCAGTTGTTTTGCACATTGCTTA (SEQ ID NO: 22)OLIGO start len tm gc % any c:\Documents and Settings\RamakrishnaMulpuri\Desktop\first 10 primers-redesigned\primer3_www_results_help.cgi-PRIMER_THREE 3′ seq (SEQ ID NOs: 23, 24) LEFT PRIMER 30 20 54.40 50.004.00 2.00 ACTGAGGCACTGAAGTTACC RIGHT PRIMER 173 20

4.00 0.00 TAAGCAATGTGCAAAACAAC SEQUENCE SIZE: 173INCLUDED REGION SIZE: 173PRODUCT SIZE: 144, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1AATTTCCATTAAATCTTGTTCGTTGCTTTACTGAGGCACTGAAGTTACCAATGTTcCACT           >>>>>>>>>>>>>>>>>>>>  61GGTTGACCTGCGGGGCTATCTCTAGGTTATGTTACTCCAGAAAATGAATTGTGTATAAAA 121GAGGCCTTGGAGGAAGGCGTTTTATTCaCATCAGTTGTTTTGCACATTGCTTA           <<<<<<<<<<<<<<<<<<<< 9) Whole sequence 

 rs1475881-rs7276487 CA/CG/GA/GG PCR did not workTCGGTTTCAGCAGGAAAGTTATTTTTAATAACTTCCCTGTATTTcTTGGTTTCAGTTATTAATTAACTCATTAATGCTAAACTTTGTGATCCTAGGTTAAAAAACATATTCAAGATAGCTTCAGAATGTTTGGTATACAAgTAGGTCTGGCTAAATATAAGTGTTAGCTTT CTCAAGCATG TAAATGCTGG (SEQ ID NO: 25)OLIGO start len 

bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 26, 27) LEFT PRIMER 10 20 48.49 25.00 5.00 3.00GCAGGAAAGTTATTTTTAAT RIGHT PRIMER 179 21 54.70 38.10 4.00 1.00TGCTTGAGAAAGCTAACACTT SEQUENCE SIZE: 191 INCLUDED REGION SIZE: 191PRODUCT SIZE: 170, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 3.00   1TCGGTTTCAGCAGGAAAGTTATTTTTAATAACTTCCCTGTATTTcTTGGTTTCAGTTATT   >>>>>>>>>>>>>>>>>>>>  61AATTAACTCATTAATGCTAAACTTTGTGATCCTAGGTTAAAAAACATATTCAAGATAGCT 121TCAGAATGTTTGGTATACAAgTAGGTCTGGCTAAATATAAGTGTTAGCTTTCTCAAGCAT              <<<<<<<<<<<<<<<<<<<< 181 CTAAATGCTGGALTERNATIVE: (LESS THAN 5 bp APART)AAGTTATTTTTAATAACTTCCCTGTATTTcTTGGTTTCAGTTATTAATTAACTCATTAATGCTAAACTTTGTGATCCTAGGTTAAAAAACATATTCAAGATAGCTTCAGAATGTTTGGTATACAAgTAGGTCTGGCTAAATATAAGTGTTAGCTTTCTCAAGCATC (SEQ ID NO: 28)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 29, 30) LEFT PRIMER 6 20 47.68 25.00 6.00 0.00ATTTTTAATAACTTCCCTGT RIGHT PRIMER 148 20 49.30 40.00 4.00 0.00CACTTATATTTAGCCAGACC SEQUENCE SIZE: 166 INCLUDED REGION SIZE: 166PRODUCT SIZE: 143, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1AAGTTATTTTTAATAACTTCCCTGTATTTcTTGGTTTCAGTTATTAATTAACTCATTAAT  >>>>>>>>>>>>>>>>>>>>  61GCTAAACTTTGTGATCCTAGGTTAAAAAACATATTCAAGATAGCTTCAGAATGTTTGGTA 121TACAAgTAGGTCTGGCTAAATATAAGTGTTAGCTTTCTCAAGCATC   <<<<<<<<<<<<<<<<<<<<10) Whole sequence 

 rs1735976-rs2827016 AA/AC/GA/GCATTCATTGTGTAGAAAGTGCCTGACTCAGTGTTTGGAAATTGTCTGACTTTTCCTCATATcTAGTGTGGTTTCATGTTATTGTATATAAGAaCTGAC

TCTGTTTACAATAATCT CCAGTGCCATAAAGACCATAATAAATAATAT (SEQ ID NO: 31)OLIGO start len tm gc % any c:\Documents and Settings\RamakrishnaMulpuri\Desktop\first 10 primers-redesigned\primer3_www_results_help.cgi-PRIMER_THREE 3′ seq (SEQ ID NOs: 32, 33) LEFT PRIMER 27 20 54.11 40.004.00 1.00 CAGTGTTTGGAAATTGTCTG RIGHT PRIMER 129 20 55.17 45.00 3.00 2.00GGCACTGGGAGATTATTGTA SEQUENCE SIZE: 152 INCLUDED REGION SIZE: 152PRODUCT SIZE: 103, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 1.00   1ATTCATTGTGTAGAAAGTGCCTGACTCAGTGTTTGGAAATTGTCTGACTTTTCCTCATAT          >>>>>>>>>>>>>>>>>>>>  61aTAGTGTGGTTTCATGTTATTGTATATAAGAaCTGACATGAACTCTGTTTACAATAATCT                <<<<<<<<<< 121 CCCAGTGCCATAAAGACCATAATAAATAATAT<<<<<<<<<< 2^(nd) group of primers 11) Whole sequence 

 rs4473479-rs2824097 CT/TC/TT (156 long)CACTGGGTCCTGTTGTTAAGTACACATAATACCAGaGAGGaGAAAATCAGGCTAATTGTAAATGGGCAACCTACTTAATTGTTTCATTAAAAAGCATACAGATTAGATTTACACTAAAGCTAGTCTTGTTTGTTTTTTTATTTTGCAAAAGTAATTACGGCCC (SEQ ID NO: 34)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 35, 36) LEFT PRIMER 8 20 47.79 35.00 6.00 2.00TCCTGTTGTTAAGTACACAT RIGHT PRIMER 163 18 53.29 44.44 8.00 2.00GGGCCGTAATTACTTTTG SEQUENCE SIZE: 163 INCLUDED REGION SIZE: 163PRODUCT SIZE: 156, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 1.00   1CACTGGGTCCTGTTGTTAAGTACACATAATACCACaCAGGAGAAAATCAGGCTAATTGTA  >>>>>>>>>>>>>>>>>>>>  61AATGGGCAACCTACTTAATTGTTTCATTAAAAAGCATACAGATTACATTTACACTAtAGC 121TAGTCTTGTTTGTTTTTTTATTTTGCAAAAGTAATTACGGCCC         <<<<<<<<<<<<<<<<<<<< 12) Whole sequence 

 rs418989-rs13047336 AC/AT/CCCTACTCAGTAGGCACTTTGTGTCTAGAAACTTCTGTGTCAACgGTTTTCCCTCTCTCTGGAATTCaTCAGGACAGAAGTGATTGGTGTGGTGGAAGAGGGTTGTGSTA (SEQ ID NO: 37)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 38, 39) LEFT PRIMER 3 21 54.40 47.62 5.00 3.00ACTCAGTAGGCACTTTGTGTC RIGHT PRIMER 97 18 54.95 50.00 2.00 0.00TCTTCCACCACACCAATC SEQUENCE SIZE: 108 INCLUDED REGION SIZE: 108PRODUCT SIZE: 95, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 2.00   1CTACTCAGTAGGCACTTTGTGTCTAGAAACTTCTGTGTCAACgGTTTTCCCTCTCTCTGG >>>>>>>>>>>>>>>>>>>> 61 AATTCaTCAGGACAGAAGTGATTGGTGTGGTGGAAGAGGGTTGTGSTA       <<<<<<<<<<<<<<<<<<<< 13) Whole sequence 

 rs987960-rs987961 AG/GG/GTTGGCTTTTCAAAGGTAAAATTTACTaAGTGTATTAATATTTTACCAATTTCCAGCCAGGAGAGTATGAATGTTGCATTATTACATTGCTTTGAAACAAAGCATTAgTCTTAATTCAGAAGTTTAAATTCAGATGTTAACGTTGC (SEQ ID NO: 40)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 41, 42) LEFT PRIMER 1 19 53.67 31.58 6.00 2.00TGGCTTTTCAAGGTAAAA RIGHT PRIMER 144 21 54.59 33.33 6.00 3.00GCAACGTTAACATCTGAATTT SEQUENCE SIZE: 144 INCLUDED REGION SIZE: 144PRODUCT SIZE: 144, PAIR ANY COMPL: 6.00, PAIR 3′ COMPL: 3.00   1TGGCTTTTCAAAGGTAAAATTTACTaAGTGTATTAATATTTTACCAATTTCCAGCCAGGA >>>>>>>>>>>>>>>>>>>> 61 GAGTATGAATGTTGCATTATTACATTGCTTTGAAACAAAGCATTAgTCTTAATTCAGAAG 121TTTAAATTCAGATGTTAACGTTGC <<<<<<<<<<<<<<<<<<<< 14) Whole sequence 

 rs4143392-rs4143391 CA/CG/GA/GGTAAGTATTGAAGAAAGGAGAATTTAAATTACTTCATATACctgataaaggaaaacatataCAAGGCAAATAAACATCTTAGATCATGACATATAAAATAATAGATTATTA (SEQ ID NO: 43)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 44, 45) LEFT PRIMER 7 30

4.00 4.00 TTGAAGAAAGGAGAATTTAA RIGHT PRIMER 98 22

22.75 6.00 3.00 ATTTTATATGTCATGATCTAAG SEQUENCE SIZE: 110INCLUDED REGION SIZE: 110PRODUCT SIZE: 92, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1TAAGTATTGAAGAAAGGAGAATTTAAATTACTTCATATACctgataaaggaaaacatata  >>>>>>>>>>>>>>>>>>>>  61CAAGGCAAATAAACATCTTAGATCATGACATATAAAATAATAGATTATTA     <<<<<<<<<<<<<<<<<<<< 15) Whole sequence 

 rs1691324-rs13050434 CG/TA/TG (4 bp apart for right primer)TGCAGAGATTACAGGTGTGAGCCACCGTGCCCAGCCTCATAACcGTTTCAACTACTTTTTCACTTGACAAGCAGATGTGAAGTTAACAAAGTCACCCATATTTGAAATAAAGATAGTATATTCCTGGGGtAGGCAGAGGCAGTTGAGGATCATGAAATAACTATG (SEQ ID NO: 46)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 47, 48) LEFT PRIMER 4 19 49.78 47.37 4.00 4.00AGAGATTACAGGTGTGAGC RIGHT PRIMER 153 19 54.61 47.37 4.00 0.00ATGATCCTCAACTGCCTCT SEQUENCE SIZE: 165 INCLUDED REGION SIZE: 165PRODUCT SIZE: 150, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 2.00   1TGCAGAGATTACAGGTGTGAGCCACCGTGCCCAGCCTCATAACcGTTTCAACTACTTTTT >>>>>>>>>>>>>>>>>>>> 61 CACTTGACAAGCAGATGTGAAGTTAACAAAGTCACCCATATTTGAAATAAAGATAGTATA 121TTCCTGGGGtAGGCAGAGGCAGTTGAGGATCATGAAATAACTATG     <<<<<<<<<<<<<<<<<<<<16) Whole sequence 

 rs11909758-rs9980111 (159 bp long) AG/AT /GTTGCAATGAAACTCAAAAGAGAAAAGTTAACAGGTGCAAaAGGTAGTTTTATTATAAAAGGAGGGTAGGCAACAAGAATATGTTTAATTTTTCTTCCTTTTCATGAGTAAGGACAAGAGTg

 (SEQ ID NO: 49)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 50, 51) LEFT PRIMER

20 49.91 30.00 3.00 0.00 TGAAACTCAAAAGAGAAAAG RIGHT PRIMER 164 20 42.7720.00 6.00 4.00 ACAGATTTCTACttaaaatt SEQUENCE SIZE: 178INCLUDED REGION SIZE: 178PRODUCT SIZE: 159, PAIR ANY COMPL: 6.00, PAIR 3′ COMPL: 3.00   1TGCAATGAAACTCAAAAGAGAAAAGTTAACAGGTGCAAaAGGTAGTTTTATTATAAAAGG >>>>>>>>>>>>>>>>>>>>  61AGGGTAGGCAACAAGAATATGTTTAATTTTTCTTCCTTTTCATGAGTAAGGACAAGAGTg 121TCATATATGTGaatatttttatttaattttaaGTAGAAATCTGTTTTTAAAATATGGG         <<<<<<<<<<<<<<<<<<<< 17) Whole sequence 

 rs

-rs

 AA/AG/TG CCACCATTCATCAAAACTTTGATACTGGACTCAATTGTGAATTTGaCTTGAAATTTGATAATGCTTTTGTTTTACTgTTCTGCTCAGCAAAATAGTACATGT (SEQ ID NO: 52)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 53, 54) LEFT PRIMER 12 20 49.40 36.00 6.00 1.00CAAAACTTTGATACTGGACT RIGHT PRIMER 102 18 48.08 31.58 6.00 1.00ACATGTACTATTTTGCTGA SEQUENCE SIZE: 102 INCLUDED REGION SIZE: 102PRODUCT SIZE: 91, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 1.00   1CCACCATTCATCAAACTTTGATACTGGACTCAATTGTGAATTTGcCTTGAAATTTGATA    >>>>>>>>>>>>>>>>>>>>  61 ATGCTTTTGTTTTACTgTTCTGCTCAGCAAAATAGTACATGT        <<<<<<<<<<<<<<<<<<<< 3^(rd) group - order primers from 18-2518) Whole sequence 

 rs2826225-rs2826226 AA/GA/GCGCCTGCATAAAGTGAGGATGGTGTAGTAATTGGGTATCTCCAGTTATAAACACAAaAAGCATGATAGAGCTGGGAcTGTGATTGCAGGAAAGCAATAGTCACTCCAAAAGGAGATCCTCATGATATGAATACGGAAGAAACAATATTTCCTGCTAATGTAGTAGCC (SEQ ID NO: 55)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 56, 57) LEFT PRIMER 2 20 58.17 50.00 4.00 0.00CCTGCATAAAGTGAGGATGG RIGHT PRIMER 120 21 59.27 47.62 6.00 0.00TGAGGATCTCCTTTTGGAGTG SEQUENCE SIZE: 166 INCLUDED REGION SIZE: 166PRODUCT SIZE: 119, PAIR ANY COMPL: 6.00, PAIR 3′ COMPL: 3.00   1GCCTGCATAAAGTGAGGATGGTGTAGTAATTGGGTATCTCCAGTTATAAACACAAaAAGC >>>>>>>>>>>>>>>>>>>> 61 ATGATAGAGCTGGGAcTGTGATTGCAGGAAAGCAATAGTCACTCCAAAAGGAGATCCTCA              <<<<<<<<<<<<<<<<<<<< 121TGATATGAATACGGAAGAAACAATATTTCCTGCTAATGTAGTAGCC 19) Whole sequence 

 rs2826842-rs232414 CA/CG/TA/TGGCAAAGGGGTACTCTATGTAATGAAcATgacctggcagtactgacatctcctgagggactgttagaagtgcagactcttgtatcttttctcaagtctatgaaatctagacttcattttaacaagatgacccgatatttacatacacattaagt (SEQ ID NO: 58)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 59, 60) LEFT PRIMER 1 20 52.04 45.00 4.00 2.00GCAAAGGGGTACTCTATGTA RIGHT PRIMER 135 20 53.29 35.00 4.00 3.00tatcgggtcatcttgttaaa SEQUENCE SIZE: 154 INCLUDED REGION SIZE: 154PRODUCT SIZE: 

, PAIR ANY COMPL: 

, PAIR 3′ COMPL: 2.00   1GCAAAGGGGTACTCTATGTAATGAAcATgacctggcagtactgacatctcctgagggact >>>>>>>>>>>>>>>>>>>> 61

<<<<< 121

<<<<<<<<<<<<<<< 20) Whole sequence 

 rs1980989-rs1980970 AA/AG/TA/TGGTATCTAACAAAGCTCTGTCCAAAATTTTGAATTTCTCGTTAAAaGCATCATGATTATAGAACAGAGGTTACAATCAATTATTCAGTCACACAATCACTCTCATCAGTCATTAAGGTGCgTACCTGGTGTTCCAGTTATTCAGTGTGGTATAACAAACTACCTGGAACTTAATG (SEQ ID NO: 61)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 62, 63) LEFT PRIMER 4 22 56.68 36.36 8.00 2.00TCTAACAAAGCTCTGTCCAAAA RIGHT PRIMER 148 21 56.12 42.86 3.00 1.00CCACACTGAATAACTGGAACA SEQUENCE SIZE: 174 INCLUDED REGION SIZE: 174PRODUCT SIZE: 145, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1GTATCTAACAAAGCTCTGTCCAAAATTTTGAATTTCTCGTTAAAaGCATCATGATTATAG >>>>>>>>>>>>>>>>>>>> 61 AACAGAGGTTACAATCAATTATTCAGTCACACAATCACTCTCATCAGTCATTAAGGTGCg 121TACCTGGTGTTCCAGTTATTCAGTGTGGTATAACAAACTACCTGGAACTTAATG  <<<<<<<<<<<<<<<<<<<< 4^(th) group 21) Whole sequence 

 rs189900-rs2221492AGAGTGGTTAAGTGACTTGATCAATTCCTCA GGTGGGGATTCAAGCTCTTAAAGCTGTAGACTATGTCGTCCAAACAAAcACTGACATGAATATGACTTCCAATAGGCAAGAAAAGAGGCCTAGGTCgAGATACTGCAAGACATGCAAGCAATCTAGTAATGGCATAAAACCTGCTATCCGAATTGGCTAAAATTATGTATT (SEQ ID NO: 64)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 65, 66) LEFT PRIMER 32 20 59.13 50.00 4.00 2.00GGTGGGGATTCAAGCTCTTA RIGHT PRIMER 100 22

2.00 GGATAGCAGGTTTTATGCCATT SEQUENCE SIZE: 202 INCLUDED REGION SIZE: 202PRODUCT SIZE: 149, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1AGAGTGGTTAAGTGACTTGATCAATTCCTCAGGTGGGGATTCAAGCTCTTAAAGCTGTAG            >>>>>>>>>>>>>>>>>>>>  61ACTATGTCGTCCAAACAAAcACTGACATGAATATGACTTCCAATAGGCAAGAAAAGAGGC 121CTAGGTCgAGATACTGCAAGACATGCAAGCAATCTAGTAATGGCATAAAACCTGCTATCC                       <<<<<<<<<<<<<<<<<<<< 181 GAATTGGCTAAAATTATGTATT22) Whole sequence 

 rs2827920-rs2827921TTCTTTCTCACACAATGGGTTCCATTCCCACTACTACTCCATTCAAATTGAAGTGCCTTCaATGATTATTAAAAAACTCTCTTTAAAATAGCTCAgGTAACCTTACATCCTTTGACTGAGGCTCAACTCATGTCAATGCTTCAGTATCAACTTTTC (SEQ ID NO: 67)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 68, 69) LEFT PRIMER 14 21

7.00 0.00 AATGGGTTCCATTCCCACTAC RIGHT PRIMER

20

7.00 1.00 TGAGCCTCAGTCAAAGGATG SEQUENCE SIZE: 156INCLUDED REGION SIZE: 156PRODUCT SIZE: 112, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1TTCTTTCTCACACAATGGGTTCCATTCCCACTACTACTCCATTCAAATTGAAGTGCCTTC     >>>>>>>>>>>>>>>>>>>>  61aATGATTATTAAAAAACTCTCTTTAAAATAGCTCAcGTAACCTTACATCCTTTGACTGAG                  <<<<<<<<<<<<<<< 121GCTCAACTCATGTCAATGCTTCAGTATCAACTTTTC <<<<< 23) Whole sequence 

 rs198047-rs2827935ATTTGTAATAACATTTAGTAAGTATTTATTTGAGGAGTTTGAATTTTGTTCTTGTTTATCTTGTTCTCTTTCTTcGTAGATTAGTTGGTGTTAACATCAATAGGATAACCCTTTCTTTCAGCATATGTGAATGAAATaAACCAATTATTGCCACTTTCCAGGTTAACCAGAATATACATAGATACGAGGACAGTGGACTGTT (SEQ ID NO: 70)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 71, 72) LEFT PRIMER

4.00 1.00 TTGAGGAGTTTGAATTTGTTC RIGHT PRIMER 164 20 57.22 40.00 3.001.00 AACCTGGAAAGTGGCAATAA SEQUENCE SIZE: 202 INCLUDED REGION SIZE: 202PRODUCT SIZE: 185, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 2.00   1ATTTGTAATAACATTTAGTAAGTATTTATTTGAGGAGTTTGAATTTTGTTCTTGTTTATC            >>>>>>>>>>>>>>>>>>>>  61TTGTTCTCTTTCTTcGTAGATTAGTTGGTGTTAACATCAATAGGATAACCCTTTCTTTCA 121GCATATGTGAATGAAATaAACCAATTATTGCCACTTTCCAGGTTAACCAGAATATACATA            <<<<<<<<<<<<<<<<<<<< 181 GATACGAGGACAGTGGACTGTT24) Whole sequence 

 rs9978999-rs9979175tagggcagagagagcaagcaagctctctaccttctcatataagggcactaatcccaccatgaaggcgccactgtcatgacCtgattatgtcacaaagaccccggggcaaatattaccactGtgaggagtacagttttagcatgtgaattttggaagaacacaaacatttag (SEQ ID NO: 73)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 74, 75) LEFT PRIMER 14 21 58.50 52.38 4.00 0.00gcaagcaagctctctaccttc RIGHT PRIMER 160 22 59.98 36.36 4.00 2.00tgttcttccaaaattcacatgc SEQUENCE SIZE: 171 INCLUDED REGION SIZE: 171PRODUCT SIZE: 147, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 0.00   1tagggcagagagagcaagcaagctctctaccttctcatataagggcactaatcccaccat       >>>>>>>>>>>>>>>>>>>>  61gaaggcgccactgtcatgacCtgattatgtcacaaagaccccggggcaaatattaccact 121Gtgaggagtacagttttagcatgtgaattttggaagaacacaaacatttag        <<<<<<<<<<<<<<<<<<<< 25) Whole sequence 

 rs1034346-rs12481852ATTCTAATTTTAAATATCATTGATGTAGAACATTCTATTTCACTATTCCTTCATTTTATTaTTATGGGAAATTATATACAGTTCTCCAGATTTTTAAAGCCTTGCTAACATGTTTTAAGTCACACAAATATTCTcCTGTGGGAAAATGACAGTAATTTAGTGTGCAACAATTATATAGAACTATTTTTCAAACTT (SEQ ID NO: 76)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 77, 78) LEFT PRIMER 37 21 50.04 23.61 2.00 0.00ATTTCACTATTCCTTCATTTT RIGHT PRIMER 173 22 50.19 27.27 6.00 3.00TAATTGTTGCACACTAAATTAC SEQUENCE SIZE: 195 INCLUDED REGION SIZE: 195PRODUCT SIZE: 137, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 2.00   1ATTCTAATTTTAAATATCATTGATGTAGAACATTCTATTTCACTATTCCTTCATTTTATT               >>>>>>>>>>>>>>>>>>>>  61aTTATGGGAAATTATATACAGTTCTCCAGATTTTTAAAGCCTTGCTAACATGTTTTAAGT 121CACACAAATATTCTcCTGTGGGAAAATGACAGTAATTTAGTGTGCAACAATTATATAGAA           <<<<<<<<<<<<<<<<<<<< 181 CTATTTTTCAAACTT 5^(th) group26) Whole sequence 

 rs7509829-rs2628358ACTGTCATGGACTTAAAGAATTGTCTTTGAATTGTCTTTTTTCATACTTTTATTTGCATCTTTcCACTAAAAAGATGgCACAAAGTAATCCTAGTTTACATTTTTTACCATGTAATTCCATATTACTTTTTCGTGAAA (SEQ ID NO: 79)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 80, 81) LEFT PRIMER 1 20 50.46 35.00 4.00 0.00ACTGTCATGGACTTAAACAA RIGHT PRIMER 137 22 63.49 27.27 4.00 0.00TTCAGGAAAAAGTAATATGGAA SEQUENCE SIZE: 138 INCLUDED REGION SIZE: 138PRODUCT SIZE: 137, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1ACTGTCATGGACTTAAACAATTGTCTTTGAATTGTCTTTTTTCATACTTTTATTTGCATC >>>>>>>>>>>>>>>>>>>> 61 TTTcCACTAAAAAGATGgCACAAAGTAATCCTAGTTTACATTTTTTACCATGTAATTCCA                      <<<<< 121 TATTACTTTTTCCTGAAA <<<<<<<<<<<<<<<6^(th) group 27) Whole sequence 

 rs4817013-rs7277036aaagaaaaaaaagccacagaaatcagtcctagcgaaaacCgatctatgagctgcctgaAaataattataaaaataactatcataaaaatgcccagtgagatataagaaaacacagacaac (SEQ ID NO: 82)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 83, 84) LEFT PRIMER 8 21 56.10 38.10 4.00 2.00aaaaagccacagaaatcagtc RIGHT PRIMER 107 22 55.60 36.36 4.00 2.00ttcttatatctcactgggcatt SEQUENCE SIZE: 119 INCLUDED REGION SIZE: 119PRODUCT SIZE: 109, PAIR ANY COMPL: 6.00, PAIR 3′ COMPL: 1.00   1

     >>>>>>>>>>>>>>>>>>>>  61ataattataaaataactatcataaaaatgcccagtgagctataagaaaacacagacaac              <<<<<<<<<<<<<<<<<<<< 26) Whole sequence 

 rs9691121-rs

CAAGGTCAGAGAAGTTATCTTGGATGGTAGAAGAGAAGAAAGGAGAAGAAaGGATAAGCAGAAAATCAAAAAGGGCATAAAAAAATTACTGGgGAAAATAATTCTTAGTCACTCACCATTTCTTATGTTTGTGAAAACAGAAA (SEQ ID NO: 85)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 86, 87) LEFT PRIMER 22 22 56.24 45.45 2.00 0.00GGATGGTAGAAGAGAAGAAAGG RIGHT PRIMER 134 22 55.74 31.82 4.00 1.00TCACAAACATAAGAAATGGTGA SEQUENCE SIZE: 143 INCLUDED REGION SIZE: 143PRODUCT SIZE: 113, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 0.00   1CAAGGTCAGAGAAGTTATCTTGGATGGTAGAAGAGAAGAAAGGAGAAGAAaGGATAAGCA        >>>>>>>>>>>>>>>>>>>>  61GAAAATCAAAAAGGGCATAAAAAAATTACTGGgGAAAATAATTCTTAGTCACTCACCATT                    <<<<<<<<<< 121 TCTTATGTTTGTGAAAACAGAAA<<<<<<<<<<<<<< 29) Whole sequence 

 rs455921-rs2898102gaccacaattcacaaatgcaaagatgcagaaccaacctaagtggccaCtgactaatgagaggataaagaagatgtggcatatataTatcagggactactactcagccattacaaggaacaaaataatgtcttttgc (SEQ ID NO: 88)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 89, 90) LEFT PRIMER 17 20 59.85 45.00 4.00 0.00tgcaaagatgcagaaccaac RIGHT PRIMER 123 22 59.63 36.36 2.00 1.00ttttgttccttgtaatggctga SEQUENCE SIZE: 138 INCLUDED REGION SIZE: 138PRODUCT SIZE: 107, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 1.00   1gaccacaattcacaaatgcaaagatgcagaaccaacctaagtggccaCtgactaatgaga       >>>>>>>>>>>>>>>>>>>>  61ggataaagaagatgtggcatatataTatcagggactactactcagccattacaaggaaca                      <<<<<<<<<<<<<<<<<<< 121 aaataatgtcttttgc <<<30) Whole sequence 

 rs2808102-rs458848gaccacaattcacaaatgcaaagatgcagaaccaacctaagtggccactgactaatgagaggataaagaagatgtggcatatataCatcagggactactTctcagccattacaaggaacaaaataatgtcttttgcaacaacttggatagagctggaggc (SEQ ID NO: 91)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 92, 93) LEFT PRIMER 17 20 59.65 45.00 4.00 0.00tgcaaagatgcagaaccaac RIGHT PRIMER 160 21 59.66 52.38 4.00 3.00gcctccagctctatccaagtt SEQUENCE SIZE: 

INCLUDED REGION SIZE: 

PRODUCT SIZE: 144, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 3.00   1gaccacaattcacaaatgcaaagatgcagaaccaacctaagtggccactgactaatgaga        >>>>>>>>>>>>>>>>>>>>  61ggataaagaagatgtggcatatataCatcagggactactTctcagccattacaaggaaca 121aaataatgtcttttgcaacaacttggatagagctggaggc           <<<<<<<<<<<<<<<<<<<<31) Whole sequence 

 rs961301-rs2830206AATCCTAGACCTTGGATTGCAAGAGACTCCTTAATATCTTCCCATGTCCACATTTcCTTCACATAGTTTGAATGTGGCTTCTATTATATACAGATACAAGATTCAAATCCAACCTCTAtGATGACTGGTCTTGTGAATAAGCAGAAGAGGCACTAACAAT (SEQ ID NO: 94)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 95, 96) LEFT PRIMER 29 22 57.95 40.91 4.00 2.00CCTTAATATCTTCCCATGTCCA RIGHT PRIMER 160 22 57.35 40.91 3.00 0.00ATTGTTAGTGCCTCTTCTGCTT SEQUENCE SIZE: 160 INCLUDED REGION SIZE: 160PRODUCT SIZE: 132, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 1.00   1AATCCTAGACCTTGGATTGCAAGAGACTCCTTAATATCTTCCCATGTCCACATTTcCTTC           >>>>>>>>>>>>>>>>>>>>  61ACATAGTTTGAATGTGGCTTCTATTATATACAGATACAAGATTCAAATCCAACCTCTAtG 121ATGACTGGTCTTGTGAATAAGCAGAAGAGGCACTAACAAT       <<<<<<<<<<<<<<<<<<<<32) Whole sequence 

 rs2174536-rs458076AAGAGAAGTGAGGTCAGCAGCTGCAAGCCACCTCCGTCATTTAGAAAAGCTTCaTGATGTAGTGTGTCGTTTCGATGTGACACTGTCTCACAGAGTTAAAATGATGTtAAGGAACTGTTCAATGGAAATTTAGAAATTTCTCTTTTTCTCAATTTTAGTGTA (SEQ ID NO: 97)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 98, 99) LEFT PRIMER 3 20 57.31 55.00 5.00 5.00GAGAAGTGAGGTCAGCAGCT RIGHT PRIMER 136 22 53.92 27.27 5.00 2.00TTTCTAAATTTCCATTGAACAG SEQUENCE SIZE: 132 INCLUDED REGION SIZE: 132PRODUCT SIZE: 134, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 2.00   1AAGAGAAGTGAGGTCAGCAGCTGCAAGCCACCTCCGTCATTTAGAAAAGCTTCaTGATGT >>>>>>>>>>>>>>>>>>>> 61 AGTGTGTCGTTTCGATGTGACACTGTCTCACAGAGTTAAAATGATGTtAAGGAACTGTTC                    <<<<<< 121 AATGGAAATTTAGAAATTTCTCTTTTCTCAATTTTAGTGTA<<<<<<<<<<<<<<<< 33) Whole sequence 

 rs432557-rs1012766ATGGCTGAATAGTATTCCCTTGTGTATATATCTaTTTATCCTTTTATTCATTGATGGACACTTAGGCTGATTTTCTCTCTTCTCATGGCTGGCTTCTCATCACCCTTTGGTCCTCCTGTATCCTCgTGTAATAAAGCTCTTCCCCAATATCTCGATAGAT (SEQ ID NO: 100)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 101, 102) LEFT PRIMER 3 22 55.77 45.45 9.00 0.00GGCTGAATAGTATTCCCTTGTG RIGHT PRIMER 155 20 59.22 50.00 4.00 2.00TCGAGATATTGGGGAAGAGC SEQUENCE SIZE: 160 INCLUDED REGION SIZE: 160PRODUCT SIZE: 

, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 1.00   1ATGGCTGAATAGTATTCCCTTGTGTATATATCTcTTTATCCTTTTATTCATTGATGGACA >>>>>>>>>>>>>>>>>>>> 61 CTTAGGCTGATTTTCTCTCTTCTCATGGCTGGCTTCTCATCACCCTTTGGTCCTCCTGTA 121TCCTCgTGTAATAAAGCTCTTCCCCAATATCTCGATAGAT      <<<<<<<<<<<<<<<<<<<<34) Whole sequence 

 rs10222076-rs10222675

CCTC CGTGTAAGAGCTGGGAAGGGAAAGTGGCTAAGTTGTGCAAATGTGCACATTGGTTGGAGATGATTAACTTCTGGCATGT (SEQ ID NO: 103)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 104, 105) LEFT PRIMER 17 22 58.32 45.45 4.00 2.00cctccacaaagactattccaga RIGHT PRIMER 146 20 50.76 55.00 4.00 2.00CACTTTCCCTTCCCAGCTCT SEQUENCE SIZE: 

INCLUDED REGION SIZE: 

PRODUCT SIZE: 130, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 3.00   1cattttaacttgattacctccacaaagactattccagaataaggttatgttctgaggtat           >>>>>>>>>>>>>>>>>>>>  61taggggttacAacttcaacatatgaattttgagtggacacaattcaacccatagcaCCTC 121CGTGTAAGAGCTGGGAAGGGAAAGTGGCTAAGTTGTGCAAATGTGCACATTGGTTGGAGA <<<<<<<<<<<<<<<<<<<< 161 TGATTAACTTCTGGCATGT 35) Whole sequence 

 rs11088023-rs11088024agggggaaattggcaatctgattctaaaattcataCggaaaaaaacaatggagttagaataactaaaacaagtccgaaaaagaaaaagaaatggaggactaatgctacctgatttcaagtcttatcTtataaatctacatcaataaaggacaagttg (SEQ ID NO: 106)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 107, 108) LEFT PRIMER 6 20 54.34 35.00 7.00 3.00gaaaattggcaatctgattct RIGHT PRIMER 157 21 51.94 33.33 5.00 0.00caacttgtcctttattgatgt SEQUENCE SIZE: 157 INCLUDED REGION SIZE: 157PRODUCT SIZE: 152, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1aggggcaaattggcaatctgattctaaaattcataCggaaaaaaacaatggagttagaat  >>>>>>>>>>>>>>>>>>>>  61aactaaaacaagtccgaaaaagaaaaagaaatggaggactaatgctacctgatttcaagt 121cttatcTtataaatctacatcaataaaggacaagttg        <<<<<<<<<<<<<<<<<<<<36) Whole sequence 

 rs1011734-rs1011733TCTGTGTTTGTCTATGTTGATAAAACATTGAAATGCCAaATAGCTCAAAGGTCATTCACTTAAGAAATCTAAGTACTGATAACATCTTAGCCCCGATTCTTCATAGGCATTGTTAAGCCTATTATAATTTTGGTCAGAGAGAAGGTAAACTATATTCCAGACAGGCATATAA (SEQ ID NO: 109)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 110, 111) LEFT PRIMER 12 22 50.06 22.73 6.00 2.00CTATGTTGATAAAACATTGAAA RIGHT PRIMER 167 20 51.08 40.00 4.00 2.00GCCTGTCTGGAATATAGTTT SEQUENCE SIZE: 173 INCLUDED REGION SIZE: 173PRODUCT SIZE: 156, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 3.00   1TCTGTGTTTGTCTATGTTGATAAAACATTGAAATGCCAcATAGCTCAAAGGTCATTCACT    >>>>>>>>>>>>>>>>>>>>  61TAAGAAATCTAAGTACTGATAACATCTTAGCCCCGATTCTTCATAGGCATTGTTAAGCCT 121ATTATAATTTTGGTtCAGAGAGAAGGTAAACTATATTCCAGACAGGCATATAA          <<<<<<<<<<<<<<<<<<<< 37) Whole sequence 

 rs2831244-rs9789838TGCAGGGCATATAATCTAAGCTGTAAACGTCCTGTcAGAAGACAACATATTCATCTTGCTAAGGTtTAAGCTATATGACTGGCACTGTGCTCAACTCAGAGTCATTGAATGAACAGTATTTATTTA (SEQ ID NO: 112)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 113, 114) LEFT PRIMER 3 23 56.40 40.91 5.00 3.00CAGGGCATATAATCTAAGCTGT RIGHT PRIMER 107 21 55.99 47.62 7.00 2.00CAATGACTCTGAGTTGAGCAC SEQUENCE SIZE: 126 INCLUDED REGION SIZE: 126PRODUCT SIZE: 

, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 2.00   1TGCAGGGCATATAATCTAAGCTGTAAACGTCCTGTcAGAAGACAACATATTCATCTTGCT >>>>>>>>>>>>>>>>>>>> 61 AAGGTTTAAGCTATATGACTGGCACTGTGCTCAACTCAGAGTCATTGAATGAACAGTATT          <<<<<<<<<<<<<<<<<<<< 121 TATTTA 38) Whole sequence 

 rs8132769-rs2831440TTCACATTATTCCCTTAAAATAAACTCTCTCCCTCCCCTCTCCCCTCTCAaCCTTGTCCCTTTGTTTATATAATGGGTAATTCGTTAATGTCAGCAGAATAGTTTTGGGGCCATAATGGCAAGTATCACGTG (SEQ ID NO: 115)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 116, 117) LEFT PRIMER 23 19 56.84 57.89 1.00 0.00AACTCTCTCCCTCCCCTCT RIGHT PRIMER 115 20 56.24 40.00 4.00 2.00TATGGCCCCAAAACTATTCT SEQUENCE SIZE: 132 INCLUDED REGION SIZE: 132PRODUCT SIZE: 93, PAIR ANY COMPL: 2.00, PAIR 3′ COMPL: 0.00   1TTCACATTATTCCCTTAAAATAAACTCTCTCCCTCCCCTCTCCCGTCTCAaCCTTGTCCC         >>>>>>>>>>>>>>>>>>>>  61TTTCTTTATATAATGGGTAATtCGTTAATGTCAGCAGAATAGTTTTGGGGCCATAATGGC              <<<<<<<<<<<<<<<<<<<< 121 AAGTATCACGTG 39) Whole sequence 

 rs8134060-rs2831524TCAGGAAGCAACAAGTACTGGGCAGATTGATACTGTAGCTaGGCTCTAGCTCTATACCTCTAGAATaaatgttacaaactagcaacttgaaagctaaacctggcccacag (SEQ ID NO: 118)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 119, 120) LEFT PRIMER 11 20 55.75 45.00 3.00 2.00ACAAGTACTGGGCAGATTGA RIGHT PRIMER 104 20 56.27 45.00 4.00 2.00gccaggtttagctttcaaagt SEQUENCE SIEZ: 110 INCLUDED REGION SIZE: 110PRODUCT SIZE: 94, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 3.00   1TCAGGAAGCAACAAGTACTGGGCAGATTGATACTGTAGCTaGGCTCTAGCTCTATACCTC   >>>>>>>>>>>>>>>>>>>>  61TAGAATaaatgttacaaactagcaacttgaaagctaaacctggcccacag          <<<<<<<<<<<<<<<<<<<< 40) Whole sequence 

 rs4817219-rs4817220tggttcttgagaattttataccaggagaaacactgtcagtCtgtattgaaaggaacagagaaaatTcgaaattaaagaagactattaaacctccaaaattctggca (SEQ ID NO: 121)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 122, 123) LEFT PRIMER 14 22

31.32 4.00 3.00

RIGHT PRIMER 104 21

33.33 3.00 2.00

SEQUENCE SIZE: 106 INCLUDED REGION SIZE: 106PRODUCT SIZE: 91, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 2.00   1tggttcttgagaattttacatcaggagaaaacactgtcagtCtgtattgaaaggaacagag        >>>>>>>>>>>>>>>>>>>>  61aaaaTTcgaaattaaagaagactattaaacctccaaaattctggca           <<<<<<<<<<<<<<<<<<<< 41) Whole sequence 

 rs2250911-rs2250997GCATCAAACTACACACTGTCATTCCTCCTTTATCTCCAAAAGCTTGAAAATTCCTCACTTGTaTCTCATTCTTTCTCTCTTAGAAAACTGATCACCTCTGATGAATTAgAACGGAATGACCAAGCTTTGGGAGAGGCAAAAGAATCTCGGTGTTAAAGACTCAGAGTTTAA (SEQ ID NO: 124)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 125, 126) LEFT PRIMER 17 22 58.65 40.91 3.00 0.00TGTCATTCCTCCTTTATCTCCA RIGHT PRIMER 144 20 59.42 45.00 4.00 2.00TTCTTTTGCCTCTCCCAAAG SEQUENCE SIZE: 171 INCLUDED REGION SIZE: 171PRODUCT SIZE: 128, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1GCATCAAACTACACACTGTCATTCCTCCTTTATCTCCAAAAGCTTGAAAATTCCTCACTT      >>>>>>>>>>>>>>>>>>>>  61GTaTCTCATTCTTTCTCTCTTAGAAAACTGATCACCTCTGATGAATTAgAACGGAATGAC 121CAAGCTTTGGGAGAGGCAAAAGAATCTCGGTGTTAAAGACTCAGAGTTTAA <<<<<<<<<<<<<<<<<<<<42) Whole sequence 

 rs2831899-rs2831900TTGAAAATTAAGAAACCCTGGCACAGTGTTGACTGGAGCCaCTTACCTTAATAGAAAATAAAGCTCACATATATCCATAATGAAAAGCAGAGACCAGCACAACCATAGTCACCTGACAGTTTtAAAATCCAAGGCCAGGATCTTCTCAACTCAGGCCCACTCA (SEQ ID NO: 127)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 128, 129) LEFT PRIMER 15 20 60.63 55.00 6.00 2.00ACCCTGGCACAGTGTTGACT RIGHT PRIMER 159 20 59.60 50.00 4.00 2.00TGGGCCTGAGTTGAGAAGAT SEQUENCE SIZE: 

INCLUDED REGION SIZE: 

PRODUCT SIZE: 145, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 1.00   1TTGAAAATTAAGAAACCCTGGCACAGTGTTGACTGGAGCCaCTTACCTTAATAGAAAATA     >>>>>>>>>>>>>>>>>>>>  61AAGCTCACATATATCCATAATGAAAAGCAGAGACCAGCACAACCATAGTCACCTGACAGT 121TTtAAAATCCAAGGCCAGGATCTTCTCAACTCAGGCCCACTCA        <<<<<<<<<<<<<<<<<<<<43) Whole sequence 

 rs2831902-rs2831903CACATAACTAATAAATTTGTAAGTATGTGCAACGGCTCACaCTTGCTTCCAGAATGGCACCTAAAAAACAGATTTACCTCTCCCCAAATTCAGATATGGAATTAAATGTAATGTCAGGAAAAaTGTCTAAGAGTTGGAAATGGGAAAAAAATGTTCTTTTGGT (SEQ ID NO: 212)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 213, 130) LEFT PRIMER 14 21 53.16 33.33 4.00 2.00AATTTGTAAGTATGTGCAACG RIGHT PRIMER 149 20 56.27 35.00 5.00 0.00TTTTTCCCATTTCCAACTCT SEQUENCE SIZE: 163 INCLUDED REGION SIZE: 163PRODUCT SIZE: 136, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 2.00   1CACATAACTAATAAATTTGTAAGTATGTGCAACGGCTCACaCTTGCTTCCAGAATGGCAC     >>>>>>>>>>>>>>>>>>>>  61CTAAAAAACAGATTTACCTCTCCCCAAATTCAGATATGGAATTAAATGTAATGTCAGGAA 121AAcTGTCTAAGAGTTGGAAATGGGAAAAAAATGTTCTTTTGGT    <<<<<<<<<<<<<<<<<<<<434) Whole sequence 

 rs

-rs2251447 AAAAAAAAAGATGAGACAGGCAGGTGCGAAAGAAATAAAAGTCAaAACTGATCCAGTTGGGAAACTCAGAATTGACAGTTAcGTGTCCTTTCATTTATTGATATTTTGAGATTCACAGGGGT (SEQ ID NO: 131)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 132, 133) LEFT PRIMER

20

2.00 2.00 AAAAGATGAGACAGGCAGGT RIGHT PRIMER 122 20 55.99 40.00

2.00 ACCCCTGTGAATCTCAAAAT SEQUENCE SIZE: 122 INCLUDED REGION SIZE: 122PRODUCT SIZE: 117, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 2.00   1AAAAAAAAAGATGAGACAGGCAGGTGCGAAAGAAATAAAAGTCAaAACTGATCCAGTTGG  >>>>>>>>>>>>>>>>>>>>  61GAAACTCAGAATTGACAGTTACGTGTCCTTTCATTTATTGATATTTTGAGATTCACAGGG                <<<<<<<<<<<<<<<<<< 121 GT << 45) Whole sequence 

 rs2832040-rs11088088GAGTTAAATAAAGCACTTGCTTCTATTGTTTGTACCTAAACTTAACAGAAcACAGTAAGTAACAAGTCATTGGGATGCAGAAAAGAAAAAAGAGAGTGAAGGAAGGAGAaAAGGTGAAGGGAGAATGGAAGAGAGGAAGGGAGGGAGGAA (SEQ ID NO: 134)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 135, 136) LEFT PRIMER 13 21 54.81 38.10 4.00 0.00GCACTTGCTTCTATTGTTTGT RIGHT PRIMER 141 20 57.37 50.00 2.00 0.00CCCTTCCTCTCTTCCATTCT SEQUENCE SIZE: 150 INCLUDED REGION SIZE: 150PRODUCT SIZE: 189, PAIR ANY COMPL: 2.00, PAIR 3′ COMPL: 0.00   1GAGTTAAATAAAGCACTTGCTTCTATTGTTTGTACCTAAACTTAACAGAAcACAGTAAGT    >>>>>>>>>>>>>>>>>>>>  61AACAAGTCATTGGGATGCAGAAAAGAAAAAAGAGAGTGAAGGAAGGAGAaAAGGTGAAGG 121GAGAATGGAAGAGAGGAAGGGAGGGAGGAA <<<<<<<<<<<<<<<<<<<< 46) Whole sequence 

 rs2832141-rs2246777aaacgagccaccagtgggAGCACTGCAGGTATCTGTGTGAGACCcGTACTTCACAACTCCTGCTTTCCCTCCATAAAGtAGCTTGCATTTTCCACATTGACTTTGCAGTTCTTTGGTATCTGTATTGGT (SEQ ID NO: 137)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 138, 139) LEFT PRIMER 14 18 58.28 61.11 6.00 2.00gtgggAGCACTGCAGGTA RIGHT PRIMER 123 21 55.85 38.10 4.00 2.00ACAGATACCAAAGAACTGCAA SEQUENCE SIZE: 129 INCLUDED REGION SIZE: 129PRODUCT SIZE: 110, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 3.00   1aaacgagccaccagtgggAGCACTGCAGGTATCTGTGTGAGACCcGTACTTCACAACTCC      >>>>>>>>>>>>>>>>>>>>  61TGCTTTCCCTCCATAAAGtAGCTTGCATTTTCCACATTGACTTTGCAGTTCTTTGGTATC                <<<<<<<<<<<<<<<<<<< 121 TGTATTGGT <<<47) Whole sequence 

 rs2832959-rs9980934TGGACACCTTTCAACTTAGAAATCATAAACAGATTCATTTaCTTAAAGTTAATGaaaagaattaacagaccctcctcaaaaaagacatatatgcagcctacaatcatatgaaaaaaagttcaacattactgttcagcaaatcaaa (SEQ ID NO: 140)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 141, 142) LEFT PRIMER 1 20 53.30 40.00 3.00 3.00TGGACACCTTTCAACTTAGA RIGHT PRIMER 134 22 50.67 27.27 8.00 3.00gaacagtaatgttgaacttttt SEQUENCE SIZE: 145 INCLUDED REGION SIZE: 145PRODUCT SIZE: 134, PAIR ANY COMPL: 7.00, PAIR 3′ COMPL: 3.00   1TGGACACCTTTCAACTTAGAAATCATAAACAGATTCATTTcCTTAAAGTTAATGaaaaga >>>>>>>>>>>>>>>>>>>> 61

<<<<<<<<<< 121 caacattactgttcagcaaatcaaa <<<<<<<<<<<<<< 7^(th) group48) Whole sequence 

 rs2833734-rs2833735TGGATACATTCCTAGAAATAGATGGAAACTGCTCTTGCAAAAAGCTAGCACATGTTAAAaATTTTAGAACAATTTGCCAAAGTTTATTTAGTCTAGTGATTTtGACAGGTTAAATGGACCCTTTGAGATCTTTTTTCCTCAAGTACAAAGGCT (SEQ ID NO: 143)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 144, 145) LEFT PRIMER 32 21

39.10 6.00 2.00 TCTTGCAAAAAGCTTAGCACA RIGHT PRIMER 137 21 57.77 38.106.00 1.00 AAAAAGATCTCAAAGGGTCCA SEQUENCE SIZE: 155INCLUDED REGION SIZE: 155PRODUCT SIZE: 105, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1TGGATACATTCCTAGAAATAGATGGAAACTGCTCTTGCAAAAAGCTTAGCACATGTTAAA            >>>>>>>>>>>>>>>>>>>>  61aATTTTAGAAACAATTTGCCAAAGTTTATTTAGTCTAGTGATTTtGACAGGTTAAATGGA                      <<<< 121 CCCTTTGAGATCTTTTTTCCTCAAGTACAAAGGCT<<<<<<<<<<<<<<<<< 49) Whole sequence 

 rs933121-rs933122GCTTTTGCTGAACATCAAGTGGTGAGCCAGGACTCAAaGCCAGATCTTCTTGTTTCCCTGTTAGGTGTtTGTAGCACAACTGGTATCTGCAGACTATGCTGCTGGAAGGGCTAGCCGTC (SEQ ID NO: 146)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 147, 148) LEFT PRIMER 1 20 55.91 40.00 8.00 3.00GCTTTTGCTGAACATCAAGT RIGHT PRIMER

3.00 3.00 CCTTCCAGCAGCATAGTCT SEQUENCE SIZE: 119INCLUDED REGION SIZE: 119PRODUCT SIZE: 109, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 1.00   1GCTTTTGCTGAACATCAAGTGGTGAGCCAGGACTCAAaGCCAGATCTTCTTGTTTCCCTG >>>>>>>>>>>>>>>>>>>> 61 TTAGGTGTtTGTAGCACAACTGGTATCTGCAGACTATGCTGCTGGAAGGGCTAGCCGTC            <<<<<<<<<<<<<<<<<<<< 50) Whole sequence 

 rs2834140-rs12626953ACTGTCCTAGAAAATCCAGGATGTGCAGTGATCAtGTATGAATGCATGGACCTGCACACACAGGAGTGAACAAAAGACCCACCCCTGCCAGGTCACCACTCATATCTCACCCCAGCCCACGCTAGCTCACaCTCCTCCCCACACACCACTGACCTCATCAT (SEQ ID NO: 149)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 150, 151) LEFT PRIMER 12 18 53.64 44.44 7.00 1.00AAATCCAGGATGTGCAGT RIGHT PRIMER 161 19 53.29 47.37 4.00 0.00ATGATGAGGTCAGTGGTGT SEQUENCE SIZE: 161 INCLUDED REGION SIZE: 161PRODUCT SIZE: 180, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 0.00   1ACTGTCCTAGAAAATCCAGGATGTGCAGTGATCA

GTATGAATGCATGGACCTGCACACA     >>>>>>>>>>>>>>>>>>>>  61CAGGAGTGAACAAAAGACCCACCCCTGCCAGGTCACCACTCATATCTCACCCCAGCCCAC 121GCTAGCTCACaCTCCTCCCCACACACCACTGACCTCATCAT        <<<<<<<<<<<<<<<<<<<<51) Whole sequence 

 rs2834485-rs3453CACATCACAGATCATAGTAAATGGCTTTAATTTTTTAaCGAAATCTCACTACTGCAAATGCATTGTTGTCCTAGCTAATGAATGCAtAGAGTATTGCCTGCAAAATAATAATTGAGATTCTATT (SEQ ID NO: 152)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 153, 154) LEFT PRIMER 3 22 52.35 36.36 4.00 0.00CATCACAGATCATAGTAAATGG RIGHT PRIMER 113 21 53.50 23/91 6.00 4.00AATTATTATTTTGCAGGCAAT SEQUENCE SIZE: 124 INCLUDED REGION SIZE: 124PRODUCT SIZE: 111, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 2.00   1CACATCACAGATCATAGTAAATGGCTTTAATTTTTTAaCGAAATCTCACTACTGCAAATG >>>>>>>>>>>>>>>>>>>> 61 CATTGTTGTCCTAGCTAATGAATGCAtAGAGTATTGCCTGCAAAATAATAATTGAGATTC            <<<<<<<<<<<<<<<<<<<< 121 TATT 8^(th) group52) Whole sequence 

 rs

-rs

TTATCCTCCACATCCTCATGAGGCAAACACCTTTCCTACCTTACCGCTCCtCAGTGGCCTCCCTGTTGCCTTCTTATTCAAGACTAAGACtCTCTAGAATGTTCTTTATCCTGAGTCCAGCTGATTGTCTATACTAATATCAGTACGGGGT (SEQ ID NO: 155)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 156, 157) LEFT PRIMER 17 20

50.00 4.00 2.00 CATGAGGCAAACACCTTTCC RIGHT PRIMER 121 22

3.00 0.00 GCTGGACTCAGGATAAAGAACA SEQUENCE SIZE: 151INCLUDED REGION SIZE: 151PRODUCT SIZE: 105, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1TTATCCTCCACATCCTCATGAGGCAAACACCTTTCCTACCTTACCGCTCCcCAGTGGCCT      >>>>>>>>>>>>>>>>>>>>  61CCCTGTTGCCTTCTTATTCAAGACTAAGACtCTCTAGAATGTTCTTTATCCTGAGTCCAG               <<<<<<<<<<<<<<<<<<<<< 121 CTGATTGTCTATACTAATATCAGTACGGGGT< 53) Whole sequence 

 rs12482363-rs2206032ATCACCTGGTTTGGTGCATCCTCGCAGAAAGAGACCCATACAGTGAAGTGGAAACACACCCAAAAGCTCTGCAATATTCCTAGAAGTTCTCGAATCTCCTCCTTAAcAGAGCTGCAGAAGGGAAACACAGACAGGAAGCACCTGTTTGACTCAgACAGCAGCCCTAATGCAGTGCCACTCAGGAGCATTCCCTCATTTGAAGACCCCCCAATTACATGAAATTATCAACCCC (SEQ ID NO: 346)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 347, 348) LEFT PRIMER 56 20 59.74 45.00 4.00 2.00ACACCCAAAAGCTCTGCAAT RIGHT PRIMER 199 20 60.59 50.00 4.00 2.00CAAATGAGGGAATGCTCCTG SEQUENCE SIZE: 232 INCLUDED REGION SIZE: 232PRODUCT SIZE: 144, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 0.00   1ATCACCTGGTTTGGTGCATCCTCGCAGAAAGAGAGCCATACAGTGAAGTGGAAACACACC                     >>>>>  61CAAAAGCTCTGCAATATTCCTAGAAGTTCTCGAATCTCCTCCTTAAcAGAGCTGCAGAAG >>>>>>>>>>>>>>>121 GGAAACACAGACAGGAAGCACCTGTTTGACTCAgACAGCAGCCCTAATGCAGTGCCACTC                      < 181AGGAGCATTCCCTCATTTGAAGACCCCCCAATTACATGAAATTATCAACCCC <<<<<<<<<<<<<<<<<<<54) Whole sequence 

 rs2776266-rs2835001agggtgcagcactttattatggaagcctgagctgactaatacaGGTGTCTcTATATCTCACTGAGGGAAAGTGACAGGAAAGTAAGAACCATTTaTGTCCAAGAGTCCAGAGGAGTCAACCAGATTCTGGGGGAAAAGAAGGTAC (SEQ ID NO: 158)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 159, 160) LEFT PRIMER 20 20 58.75 50.00 4.00 1.00tggaagcctgagctgactaa RIGHT PRIMER 149 20 59.67 60.00 4.00 3.00CCTTCTTTTCCCCCAGAATC SEQUENCE SIZE: 145 INCLUDED REGION SIZE: 145PRODUCT SIZE: 123, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1agggtgcagcactttattatggaagcctgagctgactaatacaGGTGTCTcTATATCTCA      >>>>>>>>>>>>>>>>>>>>  61CTGAGGGAAAGTGACAGGAAAGTAAGAACCATTTaTGTCCAAGAGTCCAGAGGAGTCAAC 121CAGATTCTGGGGGAAAAGAAGGTAC <<<<<<<<<<<<<<<<<<<< 55) Whole sequence 

 rs1984014-rs1984015TGAGAAT TTAGGAGAACAGAAGATCAGAGGGCTGCACaGGCTAAACTAGACAATGAGCCCATGCAAGTAAGTTAAGAGGAGAAGCGGGTAAGTATGCACCTGCTTTGTCTAGGtGACCAGCAAGCATTTAGCAATAGTCTTT TCAAAACAACAG (SEQ ID NO: 161)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 162, 163) LEFT PRIMER

22

4.00 1.00 TTAGGAGAACAGAAGATCAGAG RIGHT PRIMER 142 22 53.52 31.82 4.002.00 AAAGACTATTGCTAAATGCTTG SEQUENCE SIZE: 154 INCLUDED REGION SIZE: 154PRODUCT SIZE: 

, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 2.00   1TGAGAATTTAGGAGAACAGAAGATCAGAGGGCTGCACaGGCTAAACTAGACAATGAGCCC  >>>>>>>>>>>>>>>>>>>>  61ATGCAAGTAAGTTAAGAGGAGAAGCGGGTAAGTATGCACCTGCTTTGTCTAGGtGACCAG 121CAACCATTTAGCAATAGTCTTTTCAAAACAACAG <<<<<<<<<<<<<<<<<<<<58) Whole sequence 

 rs1014593-rs9305569GGAACTGCAGGAGATCCCTGCTGCCTTCCAGTTCATGGGATGATGGCCTCCACTTCTGCCCCTGTTTGCTTCTCCTTTCAaATCTTACATGAAGGTATACAGTTTGAAGAAGCCAGTTTGACTCCAATATCTGTGCAATGGAATACTGCTCATTAAAAAGgAATTAAACTATTGATACACACAACATGGGTGAAGATCAAACTGTCTCCTTCCCTTTGATTCAAGGGAATCTGAGAAATG (SEQ ID NO: 349)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 350, 351) LEFT PRIMER

19 59.26

2.00 0.00 ACTTCTGCCCCTGTTTGCT RIGHT PRIMER 135 21

4.00 3.00 TGATCTTCACCCATGTTGTGT SEQUENCE SIZE: 239INCLUDED REGION SIZE: 239PRODUCT SIZE: 146, PAIR ANY COMPL: 2.00, PAIR 3′ COMPL: 0.00   1GAACTGCAGGAGATCCCTGCTGCCTTCCAGTTCATGGGATGATGGCCTCCACTTCTGCCC                    >>>>>>>>>>  61CTGTTTGCTTCTCCTTTCAaATCTTACATGAAGGTATACAGTTTGAAGAAGCCAGTTTGA >>>>>>>>>121 CTCCAATATCTGTGCAATGGAATACTGCTCATTAAAAAGgAATTAAACTATTGATACACA                     <<< 181CAACATGGGTGAAGATCAAACTGTCTCCTTCCCTTTGATTCAAGGGAATCTGAGAAATG<<<<<<<<<<<<<<<<<< 57) Whole sequence 

 rs7281674-rs2835136AAACAGGCAAAATAAGCGTAGGGCTGTGTGTGCAACAGTTaATCATAAAGCCATCACCAGGAGACgTCACTGGGCGCCTTCTGGAGTCTATCCGTCCTAACTTTGC (SEQ ID NO: 164)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 165, 166) LEFT PRIMER 18 20

4.00 0.00 TAAGCGTAGGGCTGTGTGTG RIGHT PRIMER 97 31

57.14 3.00 1.00 GGACGCATAGACTCCAGAAGG SEQUENCE SIZE: 106INCLUDED REGION SIZE: 106PRODUCT SIZE: 85, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 0.00   1AAACAGGCAAAATAAGCGTAGGGCTGTGTGTGCAACAGTTaATCATAAAGCCATCACCAG     >>>>>>>>>>>>>>>>>>>>  61GAGACgTCACTGGGCGCCTTCTGGAGTCTATCCGTCCTAACTTTGC      <<<<<<<<<<<<<<<<<<<< 58) Whole sequence 

 rs13047304-rs13047322gaatgaccttggcacttttatcaaacatcaactggccacaCacaggtgagtctacttctggacaacttaTcctgttccattcatctgtatatctctatccttacac (SEQ ID NO: 167)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 168, 169) LEFT PRIMER 1 23 60.36 39.13 3.00 2.00gaatgaccttggcacttttatca RIGHT PRIMER 101 27 57.86 33.33 4.00 4.00aaggatagagatatacagatgaatgga SEQUENCE SIZE: 105 INCLUDED REGION SIZE: 105PRODUCT SIZE: 101, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1gaatgaccttggcacttttatcaaacatcaactggccacaCacaggtgagtctacttctg >>>>>>>>>>>>>>>>>>>> 61 gacacttaTcctgttccattcatctgtatatctctatccttacac       <<<<<<<<<<<<<<<<<<<< 59) Whole sequence 

 rs2635545-rs4816551CTGCTGGAATAGGCTGCTTGGCCATGTTCTTGGAAGCTACCACCATATCAaGGTAATTTCCCACACAACATTCCAGCCCCTGCTTTCCtCTCTGGCCTTATCTAGGGCCATTCCCCAACTCAGGTGAAT (SEQ ID NO: 170)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 171, 172) LEFT PRIMER 26 20 60.21

4.00 2.00 GGCCATGTTCTTGGAAGCTA RIGHT PRIMER 126 20 60.89 50.00 5.00 0.00TTCACCTGAGTTGGGGAATG SEQUENCE SIZE: 129 INCLUDED REGION SIZE: 129PRODUCT SIZE: 109, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 0.00   1CTGCTGGAATAGGCTGCTTGGCCATGTTCTTGGAAGCTACCACCATATCAaGGTAATTTC       >>>>>>>>>>>>>>>>>>>>  61CCACACAACATTCCAGCCCCTGCTTTCCcCTCTGGCCTTATCTAGGGCCATTCCCCAACT                  <<<<<<<<<<<< 121 CAGGTGAAT <<<<<<<<60) Whole sequence 

 rs2835735-rs2835736ACCTTTGTTCCATGCACCGCGCAAATACCTGGGAACCCTTaTTGCCCAACTCAAGAGCCAGAGTCCTCTGTCATCATTTTGCCTCTCTCCTAAGTGAgAGGACTGAGTGCAGACTTGGTGTTTGTGGGTGAGGCATGT (SEQ ID NO: 173)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 174, 175) LEFT PRIMER 11 18 62.22 55.56 5.00 0.00CATGCACCGCGCAAATAC RIGHT PRIMER 136 19 59.38 52.63 2.00 0.00ATGCCTCACCCACAAACAC SEQUENCE SIZE: 136 INCLUDED REGION SIZE: 136PRODUCT SIZE: 126, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 0.00   1ACCTTTGTTCCATGCACCGCGCAAATACCTGGGAACCCTTaTTGCCCAACTCAAGAGCCA   >>>>>>>>>>>>>>>>>>>>  61GAGTCCTCTGTCATCATTTTGCCTCTCTCCTAAGTGAgAGGACTGAGTGCAGACTTGGTG                      <<<< 121 TTTGTGGGTGAGGCATGT <<<<<<<<<<<<<<<<61) Whole sequence 

 rs13047608-rs2835826CTCCTGAGTCCAAGCCCTTCTCACTCACCTCTTTCTTGAACTAATTTCTTcCTGTTTTTTTCCAGTCCTCCCTTCTGTTCATGTCTCTCCTCTGCACACTTCCATTTTgTGGTTCAGAAAATGTCACCGTCCCAG TCACACTTGCCTTATGGCTGTTGT (SEQ ID NO: 176)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 177, 178) LEFT PRIMER 9 20 60.39 55.00 4.00 0.00TCCAAGCCCTTCTCACTCAC RIGHT PRIMER 136 23 59.87 50.00 3.00 1.00CTGCGACCGTGACATTTTCT SEQUENCE SIZE: 

INCLUDED REGION SIZE: 

PRODUCT SIZE: 127, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1CTCCTGAGTCCAAGCCCTTCTCACTCACCTCTTTCTTGAACTAATTTCTTcCTGTTTTTT   >>>>>>>>>>>>>>>>>>>>  61TCCAGTCCTCCCTTCTGTTCATGTCTCTCCTCTGCACACTTCCATTTTgTGGTTCAGAAA                     <<<<< 121 ATGTCACCGTCCCAGTCACACTTGCCTTATGGCTGTTGT<<<<<<<<<<<<<<< 62) Whole sequence 

 rs867998-rs17284497TGGAGAAAGTTGTTGCAAACTGCCCAGAGACCCTGGGAGTCACTCCAGTTTTCTGAAACCCAGATATTTCAGtGCCTCAGGAGAGACAAGTCCTGACCTTCTCTCCTCCAGCTCTCCCAGgAGATAGGCAAGCCCCTAACTCCCTAACTAAGCCCTTCAGACCTGAAATCCATTGAGTGGCTTCTTT (SEQ ID NO: 352)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 353, 354) LEFT PRIMER 15 18 59.35 61.11 4.00 0.00GCAAACTGCCCAGAGACC RIGHT PRIMER 147 26 60.57 55.00 2.00 2.00TTAGGGAGTTAGGGGCTTGC SEQUENCE SIZE: 

INCLUDED REGION SIZE: 

PRODUCT SIZE: 133, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 2.00   1TGGAGAAAGTTGTTGCAAACTGCCCAGAGACCCTGGGAGTCACTCCAGTTTTCTGAAACC     >>>>>>>>>>>>>>>>>>>>  61CAGATATTTCAGtGCCTCAGGAGAGACAAGTCCTGACCTTCTCTCCTCCAGCTCTCCCAG 121gAGATAGGCAAGCCCCTAACTCCCTAACTAAGCCCTTCAGACCTGAAATCCATTGAGTGG  <<<<<<<<<<<<<<<<<<<< 181 CTTCTTTAC 9^(th) group 63) Whole sequence 

 rs2836550-rs2212596CCCAGGAAGAGTGGAAAGATTAACCTTTGTGAGCCAAACCaGTGACACTTGATTACTTGACAGAACTAATCCTTCTGTCCTGATGACAGAAcTTCAACTACACAGGTACATGCAAGCTAATATCTGTTGTAA (SEQ ID NO: 179)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 180, 181) LEFT PRIMER 1 21 59.56 47.62 3.00 2.00CCCAGGAAGAGTGGAAAGATT RIGHT PRIMER 120 21 56.03 42.86 6.00 1.00TTAGCTTGCATGTACCTGTGT SEQUENCE SIZE: 132 INCLUDED REGION SIZE: 132PRODUCT SIZE: 120, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 3.00   1CCCAGGAAGAGTGGAAAGATTAACCTTTGTGAGCCAAACCaGTGACACTTGATTACTTGA >>>>>>>>>>>>>>>>>>>> 61 CAGAACTAATCCTTCTGTCCTGATGACAGAAcTTCAACTACACAGGTACATGCAAGCTAA               <<<<<<<<<<<<<<<<<<<< 121 TATCTGTTGTAA 64) Whole sequence 

 rs

-rs

GCCTGGCAAGCTAGATGGGGTGAATTTTCACCTGCCACAGcCGCAAGTCAAAGCCACCGGCTTCTCTCTTCTCCCTCCCATTGCTCCTGACAGCCAGGGTTAATATTTTGCCTCATGTAAACAGGGAGGCAtCCACCCGAGAATCTCCCCTCAGCCCACATAAGC (SEQ ID NO: 182)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 183, 184) LEFT PRIMER 9 20 55.41 40.00 4.00 2.00AGCTAGATGGGGTGAATTTT RIGHT PRIMER 158 18 61.14 61.11 3.00 3.00TGGGCTGAGGGGAGATTC SEQUENCE SIZE: 165 INCLUDED REGION SIZE: 165PRODUCT SIZE: 150, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 3.00   1GCCTGGCAAGCTAGATGGGGTGAATTTTCACCTGCCACAGaCGCAAGTCAAAGCCACCGG  >>>>>>>>>>>>>>>>>>>>  61CTTCTCTCTTCTCCCTCCCATTGCTCCTGACAGCCAGGGTTAATATTTTGCCTCATGTAA 121ACAGGGAGGCAtCCACCCGAGAATCTCCCCTCAGCCCACATAAGC       <<<<<<<<<<<<<<<<<<<<65) Whole sequence 

 rs465612-rs8131220atcaagctaattaatgttatctatcacttcAcatagttcaacctttttttgtggtgagagtactgaagatctactctcttagcaattttcaaatctaaaatacattattattaacacagtcactgtgccGtacgttagctctgaggaccttattcatttt (SEQ ID NO: 185)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 186, 187) LEFT PRIMER 1 22 47.21 22.73 6.00 4.00

RIGHT PRIMER 168 29 30.92 40.09 6.00 6.00

SEQUENCE SIZE: 

INCLUDED REGION SIZE: 

PRODUCT SIZE: 158, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 2.00   1atcaagctaattaatgttatctatcacttcAcatagttcaacctttttttgtggtgagag >>>>>>>>>>>>>>>>>>>> 61 tactgaagatctactctcttagcaattttcaaatctaaaatacattattattaacacagt 121

<<<<<<<<<<<<<<<<<<<< 66) Whole sequence 

 rs9980072-rs8130031TTTAATCTGATCATTGCCCTATGAGGTAGGgAGTATTCTGATTCCCATTTTATAAATAAGGAACCCGAGGCTTAGAGAGCATCaGTGACTTGTTCAAGGTCACCCACAGCTGTCAATTGACAGA (SEQ ID NO: 188)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 189, 190) LEFT PRIMER 1 21 55.02 33.33 6.00 2.00TTTAATCTGATCATTGCCCTA RIGHT PRIMER 111 18 57.61

6.00 1.00 AGCTGTGGGTGACCTTGA SEQUENCE SIZE: 124INCLUDED REGION SIZE: 124PRODUCT SIZE: 111, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 1.00   1TTTAATCTGATCATTGCCCTATGAGGTAGGgAGTATTCTGATTCCCATTTTATAAATAAG >>>>>>>>>>>>>>>>>>>> 61 GAACCCGAGGCTTAGAGAGCATCaGTGACTTGTTCAAGGTCACCCACAGCTGTCAAGTGA            <<<<<<<<<<<<<<<<<<<< 121 CAGA 10^(th) group67) Whole sequence 

 rs418359-rs2836926tgtcccaccattgtgtattaggtttgtagagCgtagacaacttgcctttttagtttgtaggtttctgtatcaagagaagatgtgtgtGggcctaacctagattacaggatcctggacttcaagtctga (SEQ ID NO: 191)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 192, 193) LEFT PRIMER 1 20 64.64 40.00 6.00 3.00tgtcccaccattgtgtatta RIGHT PRIMER 128 20 54.70 45.00 9.00 3.00tcagacttgaagtccaggat SEQUENCE SIZE: 128 INCLUDED REGION SIZE: 128PRODUCT SIZE: 128, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 1.00   1tgtcccaccattgtgtattaggtttgtagagCgtagacaacttgcctttttagtttgtag >>>>>>>>>>>>>>>>>>>> 61 gtttctgtatcaagagaagatgtgtgtGggcctaacctagattacaggatcctggacttc                           <<<<<<<<<<<< 121 aagtctga <<<<<<<<68) Whole sequence 

rs1101840-rs4810

4 tcatttgctaaggtcggatagctcctaattggcaaagtcaCgatgggatcccagggattctgaggatgaagcctgtgtttaataactAttatgccaAGTGAGCATTTTCAAATATATGAGAGAAATTA (SEQ ID NO: 194)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 195, 196) LEFT PRIMER 2 19 53.86 42.11 4.00 2.00catttgctaaggtcggata RIGHT PRIMER 114 20 51.56 36.00 6.00 2.00TATTTGAAAATGCTCACTtg SEQUENCE SIZE: 128 INCLUDED REGION SIZE: 128PRODUCT SIZE: 113, PAIR ANY COMPL: 6.00, PAIR 3′ COMPL: 0.00   1tcatttgctaaggtcggatagctcctaattggcaaagtcaCgatgggatcccagggattc >>>>>>>>>>>>>>>>>>>> 61 tgaggatgaagcctgtgtttaataactAttatgccaAGTGAGCATTTTCAAATATATGAG                    <<<<<<<<<<<<<<<<<<<< 121 AGAAATTA69) Whole sequence 

 rs7278447-rs7076858CATTGCTTCAGGGGTGTTAGTTTTGTGTTCaCAACTAGATTATAAACTCCTCTTGCATTCCTGATGGCAGTGACTTGAAGGCAtttatttgaagaataatagacatacagaaaggggcacatgtcataaaggtacagctggacgacttttcacaaagtg (SEQ ID NO: 197)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 198, 199) LEFT PRIMER 5 20 55.96 45.00 2.00 0.00GCTTCAGGGGTGTTAGTTTT RIGHT PRIMER 157 20 55.97 45.00 5.00 1.00cttgtgaaaagtcgtccag SEQUENCE SIZE: 159 INCLUDED REGION SIZE: 159PRODUCT SIZE: 153, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1CATTGCTTCAGGGGTGTTAGTTTTGTGTTCaCAACTAGATTATAAACTCCTCTTGCATTC >>>>>>>>>>>>>>>>>>>>  61CTGATGGCAGTGACTTGAAGGCAtttatttgaagaataatagacatacagaaaggggcac 121atgtcataaaggtacagctggacgacttttcacaaagtg          <<<<<<<<<<<<<<<<<<<<70) Whole sequence 

 rs

-rs

7001 GAGAGGATGGTGCCATCATGGAAAGCATGGGGCAGTCATGGAGATGACGGaGTAGCTCATGGAGAAgATAATGCCATCATGGAAGGCATAGTGCAGTCATGGAGATGATGGTGCAGC (SEQ ID NO: 200)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 201, 202) LEFT PRIMER 13 18 58.34 50.00 7.00 3.00CCATCATGGAAAGCATGG RIGHT PRIMER 100 20

4.00 2.00 TCATCTCCATGACTGCACTA SEQUENCE SIZE: 117INCLUDED REGION SIZE: 117PRODUCT SIZE: 96, PAIR ANY COMPL: 7.00, PAIR 3′ COMPL: 3.00   1GAGAGGATGGTGCCATCATGGAAAGCATGGGGCAGTCATGGAGATGACGGaGTAGCTCAT    >>>>>>>>>>>>>>>>>>>>  61GGAGAAgATAATGCCATCATGGAAGGCATAGTGCAGTCATGGAGATGATGGTGCAGC          <<<<<<<<<<<<<<<<<<<< 71) Whole sequence 

 rs367001-rs386095ATGGGGCAGTCATGGAGATGACGGAGTAGCTCATGGAGAAaATAATGCCATCATGGAAGGCATAGTGCAGTCATGGAGATGATGGTGCAGCTCATGGAGAAGATGGTGCCATCATGgAAGGCATGGTGCAATCATGGAGTAGACAGTGCAGCTGGGCCaagattctct (SEQ ID NO: 203)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 204, 205) LEFT PRIMER 16 20 54.33 60.00 4.00 3.00GAGATGACGGAGTAGCTCAT RIGHT PRIMER 156 18 55.17 61.11 6.00 2.00CCCAGCTGCACTGTCTAC SEQUENCE SIZE: 167 INCLUDED REGION SIZE: 167PRODUCT SIZE: 142, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 2.00   1ATGGGGCAGTCATGGAGATGACGGAGTAGCTCATGGAGAAaATAATGCCATCATGGAAGG     >>>>>>>>>>>>>>>>>>>>  61CATAGTGCAGTCATGGAGATGATGGTGCAGCTCATGGAGAAGATGGTGCCATCATGgAAG 121GCATGGTGCAATCATGGAGTAGACAGTGCAGCTGGGCCaagattctc     <<<<<<<<<<<<<<<<<<<< 72) Whole sequence 

 rs2837296-rs2837297GATGTGCCTCTCTTGTTCCAATCACAGGACAGGGGTATAAcTAGGGGCACTGTCTATACTGGCTGCACTCTGGCCAGTGCTGTCCCAgGTAGATTCATCAGGGTCTAGAGCTTCAGCTAACAGCATGA (SEQ ID NO: 206)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 207, 208) LEFT PRIMER 11 20 56.08 45.00 4.00 1.00TCTTGTTCCAATCACAGGAC RIGHT PRIMER 126 20 54.59 45.00 6.00 3.00ATGCTGTTAGCTGAAGCTCT SEQUENCE SIZE: 128 INCLUDED REGION SIZE: 128PRODUCT SIZE: 116, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1GATGTGCCTCTCTTGTTCCAATCACAGGACAGGGGTATAAcTAGGGGCACTGTCTATACT   >>>>>>>>>>>>>>>>>>>>  61GGCTGCACTCTGGCCAGTGCTGTCCCAgGTAGATTCATCAGGGTCTAGAGCTTCAGCTAA                 <<<<<<<<<<<<<< 121 CAGCATGA <<<<<< 73) Whole sequence 

 rs4239808-rs2410205AGGGCCATGGGATGATGCAGGTGGAGACTGGAGTGCTACAGCTGCAAGCAAATACATTTCTGTGCTGTGAAGCCAaCCATTTGGTGGTACTACGTTAAAACAGCTCTAGGAAATTAAACAGATGTTGCCTGTATTTTTGTTTCTCATATTACTACTCATTGTTTTAATGATGACTGTTTTATT (SEQ ID NO: 355)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 356, 357) LEFT PRIMER 19 20 57.45 55.00 4.00 2.00AGGTGGAGACTGGAGTGCTA RIGHT PRIMER 145 22 56.58 31.82 2.00 0.00AGAAACAAAAATACAGGCAACA SEQUENCE SIZE: 184 INCLUDED REGION SIZE: 184PRODUCT SIZE: 127, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 1.00   1AGGGCCATGGGATGATGCAGGTGGAGACTGGAGTGCTACAGCTGCAAGCAAATACATTTC      >>>>>>>>>>>>>>>>>>>>  61TGTGCTGTGAAGCCAcCCATTTGGTGGTACTACGTTAAAACAGCTCTAGGAAATTAAtAC 121AGATGTTGCCTGTATTTTTGTTTCTCATATTACTACTCATTGTTTTAATGATGACTGTTT<<<<<<<<<<<<<<<<<<<< 181 TATT 74) Whole sequence 

 rs2837381-rs4816672TTTTATTCATTAAGTTGAAAGCTCCTAAAGCAGAGGGACCaTATTTTTATGTCCCAACTCTCCTAAGgCCTTGCCTATGATAGCACATCTCTTCAATAGAATTGTCCT (SEQ ID NO: 209)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 210, 211) LEFT PRIMER 16 20 55.17 45.00 4.00 0.00TGAAAGCTCCTAAAGCAGAG RIGHT PRIMER 97 20

4.00 3.00 TTGAAGAGATGTGCTATCAT SEQUENCE SIZE: 100INCLUDED REGION SIZE: 100PRODUCT SIZE: 82, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 1.00   1TTTTATTCATTAAGTTGAAAGCTCCTAAAGCAGAGGGACCaTATTTTTATGTCCCAACTC      >>>>>>>>>>>>>>>>>>>>  61TCCTTAAGgCCTTGCCTATGATAGCACATCTCTTCAATAGAATTGTCCT      <<<<<<<<<<<<<<<<<<<< 11th group 75) Whole sequence 

 rs13047873-rs2837697AAAGACCAGCTTTTAGCTGAACATCAGGGCTGCCTTCAGAGTTTAATTACCGCCCTCCCCATGGGGCCAAATGAGCCATCGACTCCTCCCAAGGGGGTTCgGCTTGGTACTGATCTTTAAGTAAGTaAACGCTAAACCAGCTCATCTTAAAGCGCCCACATCTGATTTCCTGCTCTGCTGCAAGACAGTAGGTGACTGGTAATGACC (SEQ ID NO: 214)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 215, 216) LEFT PRIMER 26 20

5.00 2.00 AGGGCTGCCTTCAGAGTTTA RIGHT PRIMER 165 20

5.00 2.00 GCGCTTTAAGATGAGCTGGT SEQUENCE SIZE: 207INCLUDED REGION SIZE: 207PRODUCT SIZE: 130, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 1.00   1AAAGACCAGCTTTTAGCTGAACATCAGGGCTGCCTTCAGAGTTTAATTACCGCCCTCCCC         >>>>>>>>>>>>>>>>>>>>  61ATGGGGCCAAATGAGCCATCGACTCCTCCCAAGGGGGTTCgGCTTGGTACTGATCTTTAA 121GTAAGTaAACGCTAAACCAGCTCATCTTAAAGCGCCCACATCTGATTTCCTGCTCTGCTG     <<<<<<<<<<<<<<<<<<<< 181 CAAGACAGTAGGTGACTGGTAATGACC76) Whole sequence 

 rs455999-rs9305700ACTCTGCTCCCAGTGTGAACATGGGAAAAGTTGATTAAACTCTCTGACTTCAGATTCCTCaTGTAAAATGTGGGGAAACAGCTCTGACTTAATGGTGTCACTGTGAGGAGTAAATGAGGTAgCATATTTAAAGGATTTTGTATAGTGCTGGTGACAGTAACCAGCCAATAGATGATATAGCTAGTAATAGCA (SEQ ID NO: 217)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 218, 219) LEFT PRIMER 16 20 57.84 40.00 4.00 2.00TGAACATGGGGAAAGTTGAT RIGHT PRIMER 154 22

40.01 4.00 0.00 TCACCAGCACTATACAAAATCC SEQUENCE SIZE: 192INCLUDED REGION SIZE: 192PRODUCT SIZE: 139, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 2.00   1ACTCTGCTCCCAGTGTGAACATGGGGAAAGTTGATTAAACTCTCTGACTTCAGATTCCTC     >>>>>>>>>>>>>>>>>>>>  61aTGTAAAATGTGGGGAAACAGCTCTGACTTAATGGTGTCACTGTGAGGAGTAAATGAGGT 121AgCATATTTAAAGGATTTTGTATAGTGCTGGTGACAGTAACCAGCCAATAGATGATATAG    <<<<<<<<<<<<<<<<<<<< 181 CTAGTAATAGCA 77) Whole sequence 

 rs9976207-rs455473

tacaccaaactctttcttgcctctgtgtgcttgcccatgctgttccttctggcttcttccttcACATTCAAGTCTTGACTTAGATGTCACTTGCCAAGGGAGACCTTGGA (SEQ ID NO: 220)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 221, 222) LEFT PRIMER 12 21 54.96 47.62 4.00 0.00acttccttaactgtccactcc RIGHT PRIMER 159 19 54.64 47.37 7.00 2.00CCTTGGCAAGTGACATCTA SEQUENCE SIZE: 170 INCLUDED REGION SIZE: 170PRODUCT SIZE: 148, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 3.00   1

>>>>>>>>>>>>>>>>>>>>  61tacaccaaactctttcttgcctctgtgtgcttgcccatgctgttccttctggcttcttcc 121ttcACATTCAAGTCTTGACTTAGATGTCACTTGCCAAGGGAGACCTTGGA        <<<<<<<<<<<<<<<<<<<< 78) Whole seqence 

 rs2837807-rs2837808AAACATCCCAATAGACAAAACTCCAAGAAGAGTCAAAACAAGAATAAAGTaCAGGTCATCTTTTCTTTTGCACTCCTGACAGCACTTTGTACATGGTAATAATAATCTACCAATTAACTACATAAGCCACATGGTTTTATcATAGTGTGAAGCTTTGTATCCAGAAAGGAGAGAAGGCTCC (SEQ ID NO: 223)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 224, 225) LEFT PRIMER 23 22 56.31 36.36 3.00 0.00CCAAGAAGAGTCAAAACAAGAA RIGHT PRIMER 172 21 56.19 42.86 4.00 2.00TCTCCTTTCTGGATACAAAGC SEQUENCE SIZE: 181 INCLUDED REGION SIZE: 181PRODUCT SIZE: 160, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 1.00   1AAACATCCCAATAGACAAAACTCCAAGAAGAGTCAAAACAAGAATAAAGTaCAGGTCATC        >>>>>>>>>>>>>>>>>>>>  61TTTTCTTTTGCACTCCTGACAGCACTTTGTACATGGTAATAATAATCTACCAATTAACTA 121CATAAGCCACATGGTTTTATcATAGTGTGAAGCTTTGTATCCAGAAAGGAGAGAAGGCTC           <<<<<<<<<<<<<<<<<<<< 181 C 79) Whole sequence 

 rs9974587-rs2776356GGCAGAGGCATGGGGTGCATAGGGATATGGGGTGGGCCAGTTTGCTCCTCAGACCAGAAGGGGTGCAGGAcTCCCCCCGATCAGGATCaTGGAGAAAGGTGTGGACAGAGGAAGGGAGGGAGGGAGAAATGGCAGCTGCCCTGCAGTGG (SEQ ID NO: 226)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 227, 228) LEFT PRIMER 42 20 60.52 55.00 3.00 2.00TTGCTCCTCAGACCAGAAGG RIGHT PRIMER 116 20 59.68 50.00 4.00 2.00CTCCCTTCCTCTGTCCACAC SEQUENCE SIZE: 149 INCLUDED REGION SIZE: 149PRODUCT SIZE: 77, PAIR ANY COMPL: 6.00, PAIR 3′ COMPL: 1.00   1GGCAGAGGCATGGGGTGCATAGGGATATGGGGTGGGCCAGTTTGCTCCTCAGACCAGAAG          >>>>>>>>>>>>>>>>>>>>  61GGGTGCAGGAcTCCCCCCGATCAGGATCaTGGAGAAAGGTGTGGACAGAGGAAGGGAGGG >            <<<<<<<<<<<<<<<<<<<< 121 AGGGAGAAATGGCAGCTGCCCTGCAGTGG80) Whole sequence 

 rs2838089-rs2838090cagggactaagtgtctctgacaatacattcagccactactAcagtatgaagccagcccctcatccccaccttcagagacccctggtgcctcagattcctcggccattctggagctgctgtgCCCGAGGCTTGTGTAGTTGGAGATCATTTTGGCAGTCAGTGCTG (SEQ ID NO: 229)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 230, 231) LEFT PRIMER 12 22 55.48 40.91 5.00 2.00

RIGHT PRIMER 180 20

45.00 4.00 2.00 CTGACTGCCAAAATGATCTC SEQUENCE SIZE: 165INCLUDED REGION SIZE: 165PRODUCT SIZE: 149, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 1.00   1cagggactaagtgtctctgacaatacattcagccactactAcagtatgaagccagcccct     >>>>>>>>>>>>>>>>>>>>  61catccccaccttcagagacccctggtgcctcagattcctcggccattctggagctgctgt 121gCCCGAGGCTTGTGTAGTTGGAGATCATTTTGGCAGTCAGTGCTG       <<<<<<<<<<<<<<<<<<<< 12th group 81) Whole sequence 

 rs453592-rs380152CCTGTCTCCGTGCGTGAAAGCCGGCTCCAAAGTGCCTTCTGTCCTATCTGCCTTCcGCACCTGGCTTTCCTGAAAGAAAGAAAACGCGTGGCTTATCTTTTCACGGCACGCCACCTTCACTCTCaCTTTTTCTTTTCTAATAAATACCTCTGGATGGGTTAGTGGTAATCTCTCCTCAAAC (SEQ ID NO: 232)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 233, 234) LEFT PRIMER 24 20 50.00 60.00 4.00 1.00GCTCCAAAGTGCCTTCTGTC RIGHT PRIMER 158 20

58.00 2.00 2.00 CCACTAACCCATCCAGAGGT SEQUENCE SIZE: 181INCLUDED REGION SIZE: 181PRODUCT SIZE: 142, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1CCTGTCTCCGTGCGTGAAAGCCGGCTCCAAAGTGCCTTCTGTCCTATCTGCCTTCcGCAC        >>>>>>>>>>>>>>>>>>>>  61CTGGCTTTCCTGAAAGAAAGAAAACGCGTGGCTTATCTTTTCACGGCACGCCACCTTCAC 121TCTCaCTTTTTCTTTTCTAATAAATACCTCTGGATGGGTTAGTGGTAATCTCTCCTCAAA         <<<<<<<<<<<<<<<<<<<< 181 C 82) Whole sequence 

 rs442723-rs449888GGGAGCACAACCTAGGCCCCTCCTGGGGAGGTGGTGGAGTCAGAATCACGTAAGAGaCAAAGTTCCAGTCCCTCAGTGCCGGCTCCATTGTCCCCTGGACTTCCCTTACAAACCACAGATGCAAAGAGAGCACTTCTCgGAATCTCCAGACAGCCACGGTGGAGCACTCAACCCACGCGACCCTCGGGCGCAGGTGCT (SEQ ID NO: 235)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 236, 237) LEFT PRIMER 23 20 65.82 65.00 3.00 1.00CTGGGGAGGTGGTGGAGTCA RIGHT PRIMER 169 20 66.12 65.00 7.00 1.00GAGTGCTCCACGGTGGCTGT SEQUENCE SIZE: 

INCLUDED REGION SIZE: 

PRODUCT SIZE: 147, PAIR ANY COMPL: 7.00, PAIR 3′ COMPL: 1.00   1GGGAGCACAACCTAGGCCCCTCCTGGGGAGGTGGTGGAGTCAGAATCACGTAAGAGaCAA        >>>>>>>>>>>>>>>>>>>>  61AGTTCCAGTCCCTCAGTGCCGGCTCCATTGTCCCCTGGACTTCCCTTACAAACCACAGAT 121GCAAAGAGAGCACTTCTCgGAATCTCCACACAGCCACGGTGGAGCACTCAACCCACGCGA          <<<<<<<<<<<<<<<<<<<< 181 CCCTCGGGCGCAGGTGCT83) Whole sequence 

 rs375686-rs9976560CCTGAGAAGCTTCCAGCAAAGCACCAGCACGAACCGCCCCACCTCCCCACCTCCCCGCAAGCGTTGcCGGGACTGACAGATTACAGAGCTCTGgTCCCTCTGCACTCCTGCTGTGCCACCCCCAGGGTGTCAGAATGTGCCCCCGACACAGTTTCCAAAAG (SEQ ID NO: 238)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 239, 240) LEFT PRIMER 16 18 58.84

2.00 0.00 AAAGCACCAGCACGAACC RIGHT PRIMER 143 18 53.59 81.11 3.00 3.00GGGGCACATTCTGACACC SEQUENCE SIZE: 161 INCLUDED REGION SIZE: 161PRODUCT SIZE: 126, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 0.00   1CCTGAGAAGCTTCCAGCAAAGCACCAGCACGAACCGCCCCACCTCCCCACCTCCCCGCAA      >>>>>>>>>>>>>>>>>>>>  61GCGTTGcCGGGACTGACAGATTACAGAGCTCTGgTCCCTCTGCACTCCTGCTCTGCCACC 121CCCAGGGTGTCAGAATGTGCCCCCCACACAGTTCCAAAAG <<<<<<<<<<<<<<<<<<<<84) Whole sequence 

 rs3819900-rs3819901ATGCAGCTGCTGCGCCGGCCTGAGCTCTGATCCCTCCTCCGACCCAGCCTCACCCTGCaA

 (SEQ ID NO: 241)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 242, 243) LEFT PRIMER 20 19 57.00 57.58 6.00 0.00CTGAGCTCTGATCCCTCCT RIGHT PRIMER 186 18 57.51 58.96 2.00 0.00TTCTCCTGTCTCCGCTTG SEQUENCE SIZE: 162 INCLUDED REGION SIZE: 162PRODUCT SIZE: 139, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 0.00   1ATGGAGCTGCTGCGCCGGCCTGAGCTCTGATCCCTCCTCCGACCCAGCCTCACCCTGCaA       >>>>>>>>>>>>>>>>>>>>  61GCAGCACCATGTGGGGCTCAGAATGGGGATCTTAAGGGACCCTcCCCACAACCTCCCGAT 121AAGCCTTTCCACGGAGGGCCCAAGCGGAGACAGGAGAACACT       <<<<<<<<<<<<<<<<<<<<85) Whole sequence 

 rs10451852-rs10451853ACTTTCAGAATGTGCTGCCTTCCACGTGTGAACCAGACTGAGCTCCTTTCTGCCACTGATGTTGAATTGTCCATTTGCTCACaTCAGTGTCCACGTGGCAAATCCACAGGGCgTGGGTGGGATCCTGCAGTCTAGACAAAGCCAAGGAGCACCGCTGGAGGCCACGTTGGGCTTCCCAATCCACATGCAAACCC (SEQ ID NO: 244)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 245, 246) LEFT PRIMER 45 20 59.29 50.00 3.00 1.00CCTTTCTGCCACTGATGTTG RIGHT PRIMER 169 19 59.40 47.37 4.00 0.00TTGCATGTGGATTGGGAAG SEQUENCE SIZE: 194 INCLUDED REGION SIZE: 194PRODUCT SIZE: 146, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1ACTTTCAGAATGTGCTGCCTTCCACGTGTGAACCAGACTGAGCTCCTTTCTGCCACTGAT                 >>>>>>>>>>>>>>>>>>>>  61GTTGAATTGTCCATTTGCTCACaTCAGTGTCCACGTGGCAAATCCACAGGGCgTGGGTGG >>>> 121GATCCTGCAGTCTAGACAAAGCCAAGGAGCACCGCTGGAGGCCACGTTGGGCTTCCCAAT                   <<<<<<<<< 181 CCACATGCAAACCC <<<<<<<<<<86) Whole sequence 

 rs7278528-rs11701158TCTCCAGCCAGCGTGTCACAAAGCCGCTCACCTGCTCGTGTGAGTGTCTGAATGCACGTGTTTGAGTGTCAGaGGCGTGTGAACCACAGCAACTCAATCTTGAATAGGGGCTGGGTAAAGTGAGGCTgAGACCTCCCGGGGCTGCATTCCCAGATGGTTAAGGCATTCTAAGTCACAAGATGAGATAGGAAGTTCGCACAAGACACTGGTCAT (SEQ ID NO: 247)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 248, 249) LEFT PRIMER

20

55.00 4.00 0.00 TCACCTGCTCGTGTGAGTGT RIGHT PRIMER 163 20

50.00 4.00 2.00 CCTTAACCATCTGGGAATGC SEQUENCE SIZE: 213INCLUDED REGION SIZE: 213PRODUCT SIZE: 136, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 0.00   1TCTCCAGCCAGCGTGTCACAAAGCCGCTCACCTGCTCGTGTGAGTGTCTGAATGCACGTG          >>>>>>>>>>>>>>>>>>>>  61TTTGAGTGTCAGaGGCGTGTGAACCACAGCAACTCAATCTTGAATAGGGGCTGGGTAAAG 121TGAGGCTgAGACCTCCCGGGGCTGCATTCCCAGATGGTTAAGGCATTCTAAGTCACAAGA        <<<<<<<<<<<<<<<<<<<< 181 TGAGATAGGAAGTTCGCACAAGACACTGGTCAT87) Whole sequence 

 rs2839627-rs170916TTGAGTCCTCTTAAGTAGTTACTATAGTGGAGAACTTGAGTCATTCTTTGTAGCGTGCTTcGTAGAGCAGCGTGTTTGTTAGAAGGATTTGTTAATCCTGTATAGgGTCTTTACGAAGGCTCTTTTCATGGAAGCTTCTCTTTGTTGACTCC (SEQ ID NO: 250)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 251, 252) LEFT PRIMER 28 22 55.66 36.36 5.00 1.00TGGAGAACTTGAGTCATTCTTT RIGHT PRIMER 152 19 52.33 47.37 3.00 2.00GGAGTCAACAAAGAGAAGC SEQUENCE SIZE: 152 INCLUDED REGION SIZE: 152PRODUCT SIZE: 125, PAIR ANY COMPL: 6.00, PAIR 3′ COMPL: 3.00   1TTGAGTCCTCTTAAGTAGTTACTATAGTGGAGAACTTGAGTCATTCTTTGTAGCGTGCTT          >>>>>>>>>>>>>>>>>>>>  61cGTAGAGCAGCGTGTTTGTTAGAAGGATTTGTTAATCCTGTATAGgGTCTTTACGAAGGC 121TGTTTTCATGGAAGCTTCTCTTTGTTGACTCC      <<<<<<<<<<<<<<<<<<<<86) Whole sequence 

 rs2839628-rs234740CATTCTCTCCAGCTGCAAACTTTCTTCAACTTTCCTAAATTCTTAcTAAATTCAGAGGAATAGGATAAAGATCACTTAGAGAAAGGGTGCTTATCGACATAGCCTGAGTTTCCTTTAACCTCTCTgCAATGGGTGCTTTTAACTAGCTTCTACATGGCAAGCTGTTTCAGTTTG (SEQ ID NO: 253)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 254, 255) LEFT PRIMER 20 21

2.00 2.00 CTTTCTTCAACTTTCCTAAAT RIGHT PRIMER 150 19 50.96 42.11 4.002.00 TTGCCATGTAGAAGCTAGT SEQUENCE SIZE: 174 INCLUDED REGION SIZE: 174PRODUCT SIZE: 141, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 2.00   1CATTCTCTCCAGCTGCAAACTTTCTTCAACTTTCCTAAATTCTTAcTAAATTCAGAGGAA       >>>>>>>>>>>>>>>>>>>>  61TAGGATAAAGATCACTTAGAGAAAGGGTGCTTATGGACATAGCCTGAGTTTCCTTTAACC 121TCTCTgCAATGGGTGCTTTTAACTAGCTTCTACATGGCAAGCTGTTTCAGTTTG        <<<<<<<<<<<<<<<<<<<< 89) Whole sequence 

 rs2838239-rs2838240GGACATCTGGAACTGCACCAGCACAGAACCGACACGTTGTTAcTCATCGTCACTCGGCAGGGCTGAAGACCACCAGAACTCATGACAGGCAGACGTGCCTGGCCCAGTTGAGGATGTAGCtTCAGAGCCAAGCGCCAGTCCTGTTGGCCACGTGGGCTGGGGGCAGGATAGACCA (SEQ ID NO: 256)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 257, 258) LEFT PRIMER 17 19

57.89 2.00 0.00 ACCAGCACAGAACCGACAC RIGHT PRIMER 146 19 82.40 61.11 4.000.00 AACAGGACTGGCGCTTGG SEQUENCE SIZE: 175 INCLUDED REGION SIZE: 175PRODUCT SIZE: 129, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1GGAGATCTGGAACTGCACCAGGACAGAACCGACACGTTGTTAcTCATCGTCACTCGGCAG     >>>>>>>>>>>>>>>>>>>>  61GGCTGAAGACCACCAGAACTCATGACAGGCAGACGTGCCTGGCCCAGTTGAGGATGTAGC 121tTCAGAGCCAAGCGCCAGTCCTGTTGGCCACGTGGGCTGGGGGCAGGATAGACCA  <<<<<<<<<<<<<<<<<<<< 90) Whole sequence 

 rs630397-rs11089106GGCTGGTTCTGCCCTTGGGAGGTGGTTCCTTTGGCTGGACCAGAATGTCTGaAGATGATCAGGAGAGGGCCAAGGGTTGGGGGGTGCCCCATGTGCACCCTGAGAATTGCACCAGGCACA

CC (SEQ ID NO: 259)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 260, 261) LEFT PRIMER 14 20 61.70 55.00 3.00 0.00CTTGGGAGGTGGTTCCTTTG RIGHT PRIMER 143 18 61.16 61.11 4.00 1.00CTGCACAAGGAGGGCTGA SEQUENCE SIZE: 182 INCLUDED REGION SIZE: 182PRODUCT SIZE: 136, PAIR ANY COMPL: 6.00, PAIR 3′ COMPL: 0.00   1GGCTGGTTCTGCCCTTGGGAGGTGGTTCCTTTGGCTGGACCAGAATGTCTGaAGATGATC    >>>>>>>>>>>>>>>>>>>>  61AGGAGAGGGCCAAGGGTTGGGGGGTGCCCCATGTGCACCCTGAGAATTGCACCAGGCACA 121GtGAGCAACTTCAGCCCTCCTTGTGCAGAGCTGCAGCGTACAGTGCCAGCCCTCGCTGGC   <<<<<<<<<<<<<<<<<<<< 181 CC 91) Whole sequence 

 rs9637180-rs481767GTTCTCACTTTACTGAGAAACCTGGCAGCTTCTCAGGCCACCGCCCAGGTCACCTGCTCACCAGCAAcGTGAACCACAGGAACtGAGGCTGTGCGGGAGGCGGCTCTGCTCTGTGCTGGGCCCCCCTCCTCACTCACCCTCTTCAGTCAAAG (SEQ ID NO: 262)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 263, 264) LEFT PRIMER 11 20 57.70 50.00 5.00 5.00TACTGAGAAACCTGGCAGCT RIGHT PRIMER 166 20 54.98 50.00 3.00 0.00CTTTGACTGAAGAGGGTGAG SEQUENCE SIZE: 165 INCLUDED REGION SIZE: 165PRODUCT SIZE: 145, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 2.00   1GTTCTCACTTTACTGAGAAACCTGGCAGCTTCTCAGGCCACCGCCCAGGTCACCTGCTCA   >>>>>>>>>>>>>>>>>>>>  61CCAGCAAcGTGAACCACAGGAACtGAGGCTGTGCGGGAGGCGGCTCTGCTCTGTGCTGGG 121CCCCCCTCCTCCTCACTCACCCTCTTCAGTCAAAG     <<<<<<<<<<<<<<<<<<<<92) Whole sequence 

 rs

-rs

TTAGTATTATTATTTTCATATATATTTTTTATAATAATCATATATTCAATTTTATCATCAAGAAAAAAGTTTTAAAATTCaAAATCCTTTCATGTGCACTGTTTTAAACTtAGGTAGAAGAAAAAAAGTCACTGAAAATCCAAGATGTAATAAACAGGCCCAACAAAGGCCAACAAACTT (SEQ ID NO: 265)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 266, 267) LEFT PRIMER 45 20 48.37 20.00 5.00 3.00TTCAATTTTATCATCAAGAA RIGHT PRIMER 163 20 55.18 40.00 4.00 1.00TTGGGCCTGTTTATTACATC SEQUENCE SIZE: 180 INCLUDED REGION SIZE: 180PRODUCT SIZE: 119, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1TTAGTATTATTATTTTCATATATATTTTTTATAATAATCATATATTCAATTTTATCATCA                  >>>>>>>>>>>>>>>>>>>>  61AGAAAAAAGTTTTAAAATTCaAAATCCTTTCATGTGCACTGTTTTAAACTtAGGTAGAAG >>>> 121AAAAAAAGTCACTGAAAATCCAAGATGTAATAAACAGGCCCAACAAAGGCCAACAAACTT            <<<<<<<<<<<<<<<<<<<< 93) Whole sequence 

 rs152356-rs162355AGGGAACATGGCCTTGCCCACACAGATTTCAGACATCTGGCTCCAGAACTGTGGGAGGACACATTTCTGTTGTTTAGAACTGCaTGTTTTTTATACTTTGTTATGGCTGCCCTAGGcAACTAATACAGATATTATTTTCCACTTCTGAACTTAGCAAAATATTTTTAAAATGAAAATTCTTAAATGTTGGCACAGT (SEQ ID NO: 268)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 269, 270) LEFT PRIMER 14 20 63.24 45.00 3.00 3.00TTGCCCACACAGATTTCAGA RIGHT PRIMER 156 22 56.86 36.36 5.00 0.00TGCTAAGTTCAGAAGTGGAAAA SEQUENCE SIZE: 196 INCLUDED REGION SIZE: 196PRODUCT SIZE: 143, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 2.00   1AGGGAACATGGCCTTGCCCACACAGATTTCAGACATCTGGCTCCAGAACTGTGGGAGGAC    >>>>>>>>>>>>>>>>>>>>  61ACATTTCTGTTGTTTAGAACTGCaTGTTTTTTATACTTTGTTATGGCTGCCCTAGGcAAC 121TAATACAGATATTATTTTCCACTTCTGAACTTAGCAAAATATTTTTAAAATGAAAATTCT    <<<<<<<<<<<<<<<<<<<< 181 TAAATGTTGGCACAGT 94) Whole sequence 

 rs

-rs

CTGGATAAAGGATGCTACACGTCCCTGGTGGGACAGAGCAGGACGGCAGGGGATTTCATTAcGCCAcTCAGAATGGCAGGCAATGAAAAAACTTATAAATTGTTTATTTCCAGAATTTT (SEQ ID NO: 271)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 272, 273) LEFT PRIMER 3 30 54.33 48.00 4.00 4.00GGATAAAGGATGCTACACGT RIGHT PRIMER 120 20 40.40 20.00 4.00 0.00AAAATTCTGGAAATAAACAA SEQUENCE SIZE: 120 INCLUDED REGION SIZE: 120PRODUCT SIZE: 118, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 1.00   1CTGGATAAAGGATGCTACACGTCCCTGGTGGGACAGAGCAGGACGGCAGGGGATTTCATT >>>>>>>>>>>>>>>>>>>> 61 AcGCCAcTCAGAATGGCAGGCAATTGAAAAAACTTATAAATTGTTTATTTCCAGAATTTT               <<<<<<<<<<<<<<<<<<<< 95) Whole sequence 

 rs2838318-rs2838319TGTCAGTGGTGTAATCCGACTGTGAAAGATCAGTCTAACAAAACAGCGGGGAGAGAGAGGGCTGAATCAGAGCaACTAGGTCCAAAGCCGAGGGAACCACCAACAGATCCCCTGGTGACCCAACAAGAAATGCTCACAGTCTGGACCCAgTCAGAGTCTGCAGGACACAGCAGACATTCTGGAAGTTACAACAGCCAGGAGCAAGAGGACGCATGGCCTGACTG (SEQ ID NO: 274)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 275, 276) LEFT PRIMER 49 20 60.30 60.00 3.00 3.00GGGAGAGAGAGGGCTGAATC RIGHT PRIMER 202 21 59.00 52.36 4.00 2.00GCTCCTGGCTGTTGTAACTTC SEQUENCE SIZE: 224 INCLUDED REGION SIZE: 224PRODUCT SIZE: 154, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1TGTCAGTGGTGTAATCCGACTGTGAAAGATCAGTCTAACAAAACAGCGGGGAGAGAGAGG                    >>>>>>>>>>>>  61GCTGAATCAGAGCaACTAGGTCCAAAGCCGAGGGAACCACCAACAGATCCCCTGGTGACC >>>>>>>>121 CAACAAGAAATGCTCACAGTCTGGACCCAgTCAGAGTCTGCAGGACACAGCAGACATTCT 181GGAAGTTACAACAGCCAGGAGCAAGAGGACGCATGGCCTGACTG <<<<<<<<<<<<<<<<<<<<96) Whole sequence 

 rs915770-rs731935CGCCAGAGCACCCCTTCTCAGAACAGAAAGCGTCTCTACAaAGTGATCCGGAAGTGAGTGTGTGAGGGCGCTGCGTCCTCCCTGCTCCCCTTGGAGTTGCCCTTTCTTGCTCAGATCTGGGTGCCTTgGCCTTGTCCTGGGCCCTTCCGCAGCCCCCGGGGTGATCCCCGCTAG (SEQ ID NO: 277)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 278, 279) LEFT PRIMER 8 10

3.00 3.00 CCAGAGCACCCCTTCTCAG RIGHT PRIMER 148 18 62.95 66.67 6.00 0.00GGAAGGGCCCAGGACAAG SEQUENCE SIZE: 174 INCLUDED REGION SIZE: 174PRODUCT SIZE: 148, PAIR ANY COMPL: 6.00, PAIR 3′ COMPL: 2.00   1CGCCAGAGCACCCCTTCTCAGAACAGAAAGCGTCTCTACAaAGTGATCCGGAAGTGAGTG >>>>>>>>>>>>>>>>>>>> 61 TGTGAGGGCGCTGCGTCCTCCCTGCTCCCCTTGGAGTTGCCCTTTCTTGCTCAGATCTGG 121GTGCCTTgGCCTTGTCCTGGGCCCTCCGCAGCCCCCGGGGTGATCCCCGCTAG   <<<<<<<<<<<<<<<<<<<< Final Set 97) Whole sequence 

 rs1573338-rs1573339TATCTTACGGATTTGTCAACATCATTTGAGAAGAAGTCCATAGGCTCAGCAGATTTTTATGCCAGGTGGGCCATGGCATAAAAATGTGAAGAATGTGCTCaCTTAGACAATACcTGTGCTAAAATTGGAACAATACAGAGAAGATTAGCAAATTAAAACAATGTTAGGAAGTCAGTGTGGTGAGGTACGGTGCCTCATGCC (SEQ ID NO: 280)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 281, 282) LEFT PRIMER 47 21 59.24 42.86 3.00 1.00CAGCAGATTTTTATGCCAGGT RIGHT PRIMER 192 20 60.06 60.00 4.00 3.00CACCGTACCTCACCACACTG SEQUENCE SIZE: 201 INCLUDED REGION SIZE: 201PRODUCT SIZE: 146, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 3.00   1TATCTTACGGATTTGTCAACATCATTTGAGAAGAAGTCCATAGGCTCAGCAGATTTTTAT                  >>>>>>>>>>>>>>  61GCCAGGTGGGCCATGGCATAAAAATGTGAAGAATGTGCTCaCTTAGACAATACcTGTGCT >>>>>>> 121AAAATTGGAACAATACAGAGAAGATTAGCAAATTAAAACAATGTTAGGAAGTCAGTGTGG                    <<<<<<<< 181 TGAGGTACGGTGCCTCATGCC <<<<<<<<<<<<98) Whole sequence 

 rs3788094-rs3788095AGGCAGGGCCCTCCTTGCCACATGTAAAGCTGCACAGAGCGGTCACTATATGTGTTTCCATATTTGCAATCCAACCACCACCAACTGAGTGTGCGTCCTGaTCAGCCGAGCCTGCCCACGGTGGCCACAGGCCCTGTACATTCTAATCTCGAGAGCCTGAGCATGTACAAATTAAACgAAGCAAAACGACACCACCCAGTTCTGGCCGTACTATAGGAGGTTTCCAGGAAGGGTTTGTGAACATAAACATAAGCTAGGTAACACTCCTTTCTGAA (SEQ ID NO: 283)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 284, 285) LEFT PRIMER 13 20 67.86 60.00 5.00 3.00AACCACCACCAACTGAGTGT RIGHT PRIMER 220 20 59.94 60.00 6.00 2.00CCTCCTATAGTAGGGCCAGA SEQUENCE SIZE: 275 INCLUDED REGION SIZE: 275PRODUCT SIZE: 148, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 1.00   1AGGCAGGGCCCTCCTTGCCACATGTAAAGCTGCACAGAGCGGTCACTATATGTGTTTCCA  61TATTTGCAATCCAACCACCACCAACTGAGTGTGCGTCCTGaTCAGCCGAGCCTGCCCACG    >>>>>>>>>>>>>>>>>>>> 121GTGGCCACAGGCCCTCTACATTCTAATCTCGAGAGCCTGAGCATGTACAAATTAAACgAA 181GCAAAACGACACCACCCAGTTCTGGCCGTACTATAGGAGGTTTCCAGGAAGGGTTTGTGA       <<<<<<<<<<<<<<<<<<<< 241 ACATAAACATAAGCTAGGTAACACTCCTTTCTGAA99) Whole sequence 

 rs756554-rs756555TCAGAGCATCGCCTCAGTGGCCATCAATAGCTCGGGGGACTGGATTGCTTTTGGCTGTTCAGGTTTGTCCCCaGCCTGGGTGGTAGAGATGGACTCCCCATTAGGGACCAGTGCTGCCCGGCTACAGGCtTACTTGACAGCCACCCACTGGGGGTGCCCTCCCCTCCCCCAGTTGTCTTCCATGGGGTGCCCTCTCCCCCAGCCGCCTTTCAGAAGGGGCCCTCCCCTCC (SEQ ID NO: 286)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 287, 288) LEFT PRIMER 41 20 61.15 45.00 2.00 0.00TGGATTGCTTTTGGCTGTTC RIGHT PRIMER 189 20 61.57 55.00 6.00 2.00CACCCCATGGAAGACAACTG SEQUENCE SIZE: 230 INCLUDED REGION SIZE: 230PRODUCT SIZE: 149, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 2.00   1TCAGAGCATCGCCTCAGTGGCCATCAATAGCTCGGGGGACTGGATTGCTTTTGGCTGTTC               >>>>>>>>>>>>>>>>>>>>  61AGGTTTGTCCCCaGCCTGGGTGGTAGAGATGGACTCCCCATTAGGGACCAGTGCTGCCCG 121GCTACAGGCtTACTTGACAGCCACCCACTGGGGGTGCCCTCCCCTCCCCCAGTTGTCTTC                   <<<<<<<<<<< 181CATGGGGTGCCCTCTCCCCCAGCCGCCTTTCAGAAGGGGCCCTCCCCTCC <<<<<<<<<100) Whole sequence 

 rs

-rs

CTCATGCTTACATCCTTAGCTGATCATTAAACTTTGTGACCATTTCATGCTCACTGCTTTCTTGCCcGGGAGCTAATGGTGAGGAAAGGTCACTGGGAACCAGCCCACCAACCTCAGACATcGATTTTGTTCCAGGCTTTTTTCCTGGGCAGGGGTGGCTATCACCTGCTGGTAGGCAGCGGCAGGCCCACTGTCCTGC (SEQ ID NO: 289)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 290, 291) LEFT PRIMER 27 21 53.45 28.57 5.00 2.00TTAAACTTTGTGACCATTTCA RIGHT PRIMER 174 18 54.56 65.58 6.00 2.00TACCAGCAGGTGATAGCC SEQUENCE SIZE: 199 INCLUDED REGION SIZE: 199PRODUCT SIZE: 148, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 0.00   1CTCATGCTTACATCCTTAGCTGATCATTAAACTTTGTGACCATTTCATGCTCACTGCTTT          >>>>>>>>>>>>>>>>>>>>  61CTTGCCcGGGAGCTAATGGTGAGGAAAGGTCACTGGGAACCAGCGCACCAACCTCAGACA 121TcGATTTTGTTCCAGCCTTTTTTCCTGGGCAGGGGTGGCTATCACCTGCTGGTAGGCAGC              <<<<<<<<<<<<<<<<<<<< 181 GGCAGGCCCACTGTCCTGC101) Whole sequence 

 rs2838551-rs2838552TGACACAAAAGTCTCAGAGCAGTCCCTTCTGAGCTCTTCTACACCAAGCAGGCAGAATGTTCACTGCTAATGAGgCTGGAGCTGGTCCCCAGCAGTGGTAGGAAGCTTCCAaCAGGCTCAGGCTGTGGGTGCTTGCAGGGGCACAGTGTGACGGCCACGGGCCTCAGAGCTCTGGTGGGCT (SEQ ID NO: 292)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 293, 294) LEFT PRIMER 2

53.05 45.00 5.00 3.00 GACAGAAAAGTCTCAGAGCA RIGHT PRIMER 135 18 62.1061.11 5.00 3.00 CAAGCACCCACAGCCTGA SEQUENCE SIZE: 181INCLUDED REGION SIZE: 181PRODUCT SIZE: 124, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 3.00   1TGACAGAAAAGTCTCAGAGCAGTGCCTTCTGAGCTCTTCTACACCAAGCAGGCAGAATGT >>>>>>>>>>>>>>>>>>>> 61 TCACTGCTAATGAGgCTGGAGCTGGTCCCCAGCAGTGGTAGGAAGCTTCCAaCAGGCTCA                      <<< 121GGCTGTGGGTGCTTGCAGGGGCACAGTGTGACGGCCACGGGCCTCAGAGCTCTGGTGGGC<<<<<<<<<<<<<<< 181 T 102) Whole sequence 

 rs8134902-rs8133874ACATCTTTCTCAAATAAAGATAACAGCGATGTATTTTCACAAAAGCAAGAGCTTAGAAAGTACTcCACCCAGGTATCCCTCTTGGAAAAAATaCTTAAGGAAATATGACAAATGGCAAAGTGATTGTTATGGATGGAATGTTTGTATCCTCCCAAAATTCACATGTTGAGACCCTAATTCCAATATG (SEQ ID NO: 295)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 296, 297) LEFT PRIMER 53 30 54.64 38.00 6.00 2.00ATTTTCACAAAAGCAAGAGC RIGHT PRIMER 155 20 54.97 40.00 3.00 0.00TTGGGAGGATACAAACATTC SEQUENCE SIZE: 187 INCLUDED REGION SIZE: 187PRODUCT SIZE: 128, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1ACATCTTTCTCAAATAAAGATAACAGCGATGTATTTTCACAAAAGCAAGAGCTTAGAAAG            >>>>>>>>>>>>>>>>>>>>  61TACTcCACCCAGGTATCCCTCTTGGAAAAAATaCTTAAGGAAATATGACAAATGGCAAAG 121TGATTGTTATGGATGGAATGTTTGTATCCTCCCAAAATTCACATGTTGAGACCCTAATTC     <<<<<<<<<<<<<<<<<<<< 181 CAATATG 103) Whole sequence 

 rs425667-rs362478AGGGGCATTCTACAAAACACCCAACCGGTCAAGGTCGCTGAGGCCAAGGAGAGATTGGGCAACCGTCACAAACCAGAGAAGcCGAGGAGAcCTTTCAGCCAACGCCATGTGGGGTCCTGAGCAGGACCCACCGGAAGTTGGTGCAGCTGCCTAAAGACCGTCCTGGCTGAGAAGAAACAG (SEQ ID NO: 298)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 299, 300) LEFT PRIMER 46 16 55.06 50.00 4.00 2.00AAGGAGAGATTGGGCAAC RIGHT PRIMER 178 19 54.85 52.63 3.00 1.00GTTTCTTCTCAGCCAGGAC SEQUENCE SIZE: 180 INCLUDED REGION SIZE: 180PRODUCT SIZE: 133, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1AGGGGCATTCTACAAAACACCCAACCGGTCAAGGTCGCTGAGGCCAAGGAGAGATTGGGC                 >>>>>>>>>>>>>>>  61AACCGTCACAAACCAGAGAAGcCGAGGAGAcCTTTCAGCCAACGCCATGTGGGGTCCTGA >>> 121GCAGGACCCACCGGAAGTTGGTGCAGCTGCCTAAAGACCGTCCTGGCTGAGAAGAAACAG                 <<<<<<<<<<<<<<<<<<<< 104) Whole sequence 

 rs2838650-rs2838651TGGCCCTGACGTGCCAGAGCTGTTGGCCTCCAGCTGGCGGGTAAAACCCACGGCCTTCTCAGAACAGGTTTCTCAACACATGAGACAGAACACACCAGACTTCCAAGGGGAACACCTGGATGGAGCTGGTTACCCAGATcGTTCAACACCGAGGGGCAGCGGCTTGAGGGTCTTTCCACGAAGGCTTGGATTAACAAGAGGAGCASRGGTCTCTCCAGGATGGGCCCA (SEQ ID NO: 301)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 302, 303) LEFT PRIMER 79 20 54.89 50.00 4.00 1.00CATGAGACAGAACACACCAG RIGHT PRIMER 100 20 54.51 40.00 5.00 3.00TCTTGTTAATCCAAGCGTTC SEQUENCE SIZE: 229 INCLUDED REGION SIZE: 229PRODUCT SIZE: 121, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1TGGCCCTGACCTGCCAGAGCTGTTGGCCTCCAGCTGGCGGGTAAAACCCACGGCCTTCTC  61AGAACAGGTTTCTCAACACATGAGACAGAACACACCAGACTTCCaAGGGGAACACCTGGA      >>>>>>>>>>>>>>>>>>>> 121TGGAGCTGGTTACCCAGATcGTTCAACACCGAGGGGCAGCGGCTTGAGGGTCTTTCCACG                      < 181AAGGCTTGGATTAACAAGACGAGCASRGGTCTCTCCAGGATGGGCCCA <<<<<<<<<<<<<<<<<<<<105) Whole sequence 

rs2838854-rs1296489CCACCCAGTGTCACGTCACGGCCCCGGCACGCCATCCACGGACCCTGGATGGAGCCCAGCTGCCTCCaGGAGCGCAGTTTAACTACAAAGGAGCCCTGGCTGCCCGCCCCGCCCAGACGCACTGACCTGTTGTTCTCTGTGGCTGCTGATGGCCCaTCCCCAACCACTGGTGACTCTTCCCTGGGGCCCCAAGCTCAGCCCCTAACCCCCTGTTGCTGGAAGT (SEQ ID NO: 304)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 305, 306) LEFT PRIMER 37 18 65.56 66.67 5.00 2.00CACGGACCCTGGATGGAG RIGHT PRIMER 183 18 53.14 55.56 3.00 2.00CAGGGAAGAGTCACCAGT SEQUENCE SIZE: 223 INCLUDED REGION SIZE: 223PRODUCT SIZE: 147, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 2.00   1CCACCCAGTGTCACGTCACGGCCCCGGCACGCCATCCACGGACCCTGGATGGAGCCCAGC       >>>>>>>>>>>>>>>>>>>>  61TGCCTCCaGGAGCGCAGTTTAACTACAAAGGAGCCCTGGCTGCCCGCCCCGCCCAGACGC 121ACTGACCTGTTGTTCTCTGTGGCTGCTGATGGCCCaTCCCCAACCACTGGTGACTCTTCC                 <<<<<<<<<<<<<<< 181CTGGGGCCCCAAGCTCAGCCCCTAACCCCCTGTTGCTGGAAGT <<< 106) Whole sequence 

 rs2838659-rs1108261CAGAGGACTGGGCTGCGGGGTCAGGAATGGGCACACTTCCTAACTGCAGGACACTCTAAGGGCTTTGGTCATGCACACgCAGCCAAGAGAAGGTGTCGCTGaCACACAGCCTTCCAGGAGCGGACTTGGAGACCTCGCCAAGGACCAGGACTCCCCAGCACTCACACTCCCTTAGGCGCTGAAGTC (SEQ ID NO: 307)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 308, 309) LEFT PRIMER 53 20

45.00 4.00 2.00 ACTCTAAGGGCTTTGGTCAT RIGHT PRIMER 175 20 56.02 55.003.00 1.00 CTAAGGGAGTGTGAGTGCTG SEQUENCE SIZE: 186INCLUDED REGION SIZE: 186PRODUCT SIZE: 129, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1CAGAGGACTGGGCTGCGGGGTCAGGAATGGGCACACTTCCTAACTGCAGGACACTCTAAG                   >>>>>>>>  61GGCTTTGGTCATGCACACgCAGCCAAGAGAAGGTGTCGCTGaCACACAGCCTTCCAGGAG >>>>>>>>>>>>121 CGGACTTGGAGACCTCGCCAAGGACCAGGACTCCCCAGCACTCACACTCCCTTAGGCGCT                  <<<<<<<<<<<<<<<<<<<< 181 GAAGTC 107) Whole sequence 

 rs585587-rs585601GAAGAGGACAACACGGGGCTGTCTGCAGAGCACCTGCCACGCGCCAGGCTCTGTGTCCACAAGCACGGCGGCTGCTCCCACATGACaGAGCTCGTGcGGCAGCTCCAGGACTGTCTGGTGCCAGAGCCCCAGCTCTCCGCCAGCCCCAGGCCACTGTGCGAGGCCCTCAGTGAAGAGGGGGCCGT (SEQ ID NO: 310)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 311, 312) LEFT PRIMER 40 18 64.78 58.87 3.00 2.00CGCCAGGCTCTGTGTCCA RIGHT PRIMER 183 18 60.76 66.67 5.00 3.00GGCCCCCTCTTCACTGAG SEQUENCE SIZE: 185 INCLUDED REGION SIZE: 185PRODUCT SIZE: 162, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 3.00   1GAAGAGGACAACACGGGGCTGTCTGCAGAGCACCTGCCACGCGCCAGGCTCTGTGTCCAC                >>>>>>>>>>>>>>>>>>>>  61AAGCACGGCGGCTGCTCCCACATGACaGAGCTCGTGcGGCAGCTCCAGGACTGTCTGGTG 121CCAGAGCCCCAGCTCTCCGCCAGCCCCAGGCCACTGTGCGAGGCCCTCAGTGAAGAGGGG                <<<<<<<<<<<<<<< 181 GCCGT <<< 108) Whole sequence 

 rs9981033-rs4818996TCTAAATAATGTTAATGATCAAATTTAGTCAGATCTCAATCTTCATATGTTAGTTGCCTTCTTAaTAAATATTCTGTTTTCTTTATCGTTCTTTATTTGTATCTCcACCTTCATTTCTGATTAAATTAAGAAGTTTTGTCTCTTCCATTTAATAATTAATGTATTTAATAACC (SEQ ID NO: 313)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 314, 315) LEFT PRIMER 24 22 51.86 31.82 6.00 2.00TTTAGTCAGATCTCAATCTTCA RIGHT PRIMER 149 22 54.02 31.82 4.00 3.00AATTGGAAGAGACAAAACTTCTT SEQUENCE SIZE: 173 INCLUDED REGION SIZE: 173PRODUCT SIZE: 128, PAIR ANY COMPL: 6.00, PAIR 3′ COMPL: 1.00   1TCTAAATAATGTTAATGATCAAATTTAGTCAGATCTCAATCTTCATATGTTAGTTGCCTT         >>>>>>>>>>>>>>>>>>>>  61CTTAaTAAATATTCTGTTTTCTTTATCGTTCTTTATTTGTATCTCcACCTTCATTTCTGA 121TTAAATTAAGAAGTTTTGTCTCTTCCATTTAATAATTAATGTATTTAATAACC  <<<<<<<<<<<<<<<<<<<< 109) Whole sequence 

 rs2838802-rs2838803CACACTCCACACTGGCCCCACGCGGGTGGCGAAGGACTCAGCCAGAGCCTGGCAGGATCCTGGGGTGTCTaTTTCCAAGGAATGTTCTGGAAGAAACATACACACATACTTGTTTGCCAGATTTACCTGTGTGGTaTTCCAGATGAGAAGCAGCCTGTGTCACTCCATAAGGGAGAGTGCGTGCAGCATTGAGA (SEQ ID NO: 316)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 317, 318) LEFT PRIMER 31 18 56.68 51.11 5.00 3.00GAAGGACTCAGCCAGAGC RIGHT PRIMER 177 20 55.20 50.00 7.00 3.00CTCTCCCTTATGGAGTGACA SEQUENCE SIZE: 194 INCLUDED REGION SIZE: 194PRODUCT SIZE: 147, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1CACACTCCACACTGGCCCCACGCGGGTGGCGAAGGACTCAGCCAGAGCCTGGCAGGATCC           >>>>>>>>>>>>>>>>>>>>  61TGGGGTGTCTaTTTCCAAGGAATGTTCTGGAAGAAACATACACACATACTTGTTTGCCAG 121ATTTACCTGTGTGGTcTTCCAGATGAGAAGCAGCCTGTGTCACTCCATAAGGGAGAGTGC              <<<<<<<<<<<<<<<<<<<< 181 GTGCAGCATTGAGA110) Whole sequence 

 rs2183596-rs2150452AAGAAACTCCCAAGGAACGCATTGTCCCAAGTTGCTGCACCAGTCAGTGTACATTCCCACAAaCAGTGCATGAGAGTTCCTGTTGCTTGTGAAATAAATGGTCAGCATTCAGTGTTGTCAGCTTTTAAAATTTTCTCCTTTCTAGTGGGCATGTAATGGTcTCACATTATAGTTTTAATTTGCATTTTCCTGGTGACATGTGATACGGAACCTTCCTCCCATGCT (SEQ ID NO: 319)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 320, 321) LEFT PRIMER 39 19 50.19 47.37 5.00 2.00ACCAGTCAGTGTACATTCC RIGHT PRIMER 190 19 50.52 28.32 4.00 0.00GGAAAATGCAAATTAAAAC SEQUENCE SIZE: 225 INCLUDED REGION SIZE: 225PRODUCT SIZE: 152, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1AAGAAACTCCCAAGGAACGCATTGTCCCAAGTTGCTGCACCAGTCAGTGTACATTCCCAC                              >>>>>>>>>>>>>>>>>>>>  61AAaCAGTGCATGAGAGTTCCTGTTGCTTGTGAAATAAATGGTCAGCATTCAGTGTTGTCA 121GCTTTTAAAATTTTCTCCTTTCTAGTGGGCATGTAATGGTcTCACATTATAGTTTTAATT             <<<<<<<<< 181 TGCATTTTCCTGGTGACATGTGATACGGAACCTTCCTCCCATGCT<<<<<<<<<< 111) Whole sequence 

 rs

-rs

GTGCAATTTAATTACAAACGCTTAAATGGGGAGGTCAGGGGCAGAGGGATGATGTCACAAACACACCCAcGTGTGCTTGGTGCAAAACAGTAAAACAAACAGCAAGAAGgTCCATGAAGGAAAGATCGCCTCTGTCAGTGGGAGTAATGAGAGTGGCTGATGGACAGGTG (SEQ ID NO: 322)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 323, 324) LEFT PRIMER 19 20 61.86 55.00 4.00 1.00CGCTTAAATGGGGAGGTCAG RIGHT PRIMER 168 20 60.83 60.00 3.00 0.00CCTGTCCATCAGCCACTCTC SEQUENCE SIZE: 170 INCLUDED REGION SIZE: 170PRODUCT SIZE: 150, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 2.00   1GTGCAATTTAATTACAAACGCTTAAATGGGGAGGTCAGGGGCAGAGGGATGATGTCACAA      >>>>>>>>>>>>>>>>>>>>  61ACACACCCAcGTGTGCTTGGTGCAAAACAGTAAAACAAACAGCAAGAAGgTCCATGAAGG 121AAAGATCGCCTCTGTCAGTGGGAGTAATGAGAGTGGCTGATGGACAGGTG          <<<<<<<<<<<<<<<<<<<< 112) Whole sequence 

 rs11702503-rs3827270ACGCCAAGCAGGAGATGCCAGACACAGAGTCCATCCTGAGAGAGTCTGTTCCTGTCCAAGCTCAGAAACACAGGAAGCcACCTGTGCTGTAGCAGCACaCGGAGATGCATCCTTTCTGGTCCACCCCACGGCCCTCATTGCAGTCAGGGATCCTCTCCCAGAAAGTCCCTGCTGCCAGCCCCTGCCCTT (SEQ ID NO: 325)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 326, 327) LEFT PRIMER 7 20 62.02 55.00 3.00 0.00AGCAGGAGATGCCAGACACA RIGHT PRIMER 125 20 63.37 55.00 5.00 4.00GGTGGACCAGAAAGGATGCA SEQUENCE SIZE: 

INCLUDED REGION SIZE: 

PRODUCT SIZE: 119, PAIR ANY COMPL: 3.00, PAIR 3′ COMPL: 0.00   1ACGCCAAGCAGGAGATGCCAGACACAGAGTCCATCCTGAGAGAGTCTGTTCCTGTCCAAG  >>>>>>>>>>>>>>>>>>>>  61CTCAGAAACACAGGAAGCcACCTGTGCTGTAGCAGCACaCGGAGATGCATCCTTTCTGGT                 <<<<<<<<<<<<<<< 121CCACCCCACGGCCCTCATTGCAGTCAGGGATCCTCTCCCAGAAAGTCCCTGCTGCCAGCC <<<<< 181CCTGCCCTT 113) Whole sequence 

 rs2839084-rs9964302CATGAGAAAGACTTTGTTCCCATGAGAACAACAAGAGAAACTCAAACAAAATTAAAATTGTACTTTTCTAAAAGACcGGGGTGGGGGTCGTGGTCAGGCAGCaGCATGAAGAAAGCCTTGAGAACTGAATTCCAGAAAGAACAAGCATAGGCAAGAAAGAGAGATGACA (SEQ ID NO: 328)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 329, 330) LEFT PRIMER 19 22 59.21 40.91 4.00 0.00CCCATGAGAACAACAAGAGAAA RIGHT PRIMER 162 20 55.46 45.00 4.00 2.00CTCTTTCTTGCCTATGCTTG SEQUENCE SIZE: 170 INCLUDED REGION SIZE: 170PRODUCT SIZE: 144, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 3.00   1CATGAGAAAGACTTTGTTCCCATGAGAACAACAAGAGAAACTCAAACAAAATTAAAATTG       >>>>>>>>>>>>>>>>>>>>  61TACTTTTCTAAAAGACcGGGGTGGGGGTCGTGGTCAGGCAGCaGCATGAAGAAAGCCTTG 121AGAACTGAATTCCAGAAAGAAACAAGCATAGGCAAGAAAGAGAGATGACA        <<<<<<<<<<<<<<<<<<<< 114) Whole sequence 

 rs2249057-rs2249060AAGATTTAGAACAGCTGAAGCAGCGAGAAAAAACCCAGCATGAGTCaGAACTGGAGCAACTGAGGATTTATTTTGAAAAGAAGTTAAGGGATGCTGAGAAAACTTACCAAGAAGACCTAAcCCTGTTACAGCAGAGGCTGCAGGGGGCGAGGGAAGATGCTCTTCTG (SEQ ID NO: 331)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 332, 333) LEFT PRIMER 12 21 63.07 47.62 6.00 0.00CAGCTGAAGCAGCGAGAAAAA RIGHT PRIMER 146 19 66.33 68.42 6.00 3.00CCCCTGCAGCCTCTGCTGT SEQUENCE SIZE: 167 INCLUDED REGION SIZE: 167PRODUCT SIZE: 125, PAIR ANY COMPL: 7.00, PAIR 3′ COMPL: 1.00   1AAGATTTAGAACAGCTGAAGCAGCGAGAAAAAACCCAGCATGAGTCaGAACTGGAGCAAC    >>>>>>>>>>>>>>>>>>>>  61TGAGGATTTATTTTGAAAAGAAGTTAAGGGATGCTGAGAAAACTTACCAAGAAGACCTAA 121cCCTGTTACAGCAGAGGCTGCAGGGGGCGAGGGAAGATGCTCTTCTG   <<<<<<<<<<<<<<<<<<<<115) Whole sequence 

 rs2839226-rs2839227GGGAAACTGACTTGGCTTTTGCAAGGGTCATTGCTTCCTGATGCATGTTTAACTGTCCTGTGTTCACTTTGTTGCcGCAGGTTTTTAGAGGAACGTAAAGAGATCaCCGAGAAATTCAGTGCGGAACAAGATGCCTTCCTGCAGGAGGCCCAGGAGCAGCATGCCCGTGAGCTG (SEQ ID NO: 334)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 335, 336) LEFT PRIMER 1 22 64.29

3.00 2.00 GGGAAACTGACTTGGCTTTTGC RIGHT PRIMER 135 20 64.33

2.00 2.00 GGCATCTTGTTCCGCACTGA SEQUENCE SIZE: 174INCLUDED REGION SIZE: 174PRODUCT SIZE: 125, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1GGGAAACTGACTTGGCTTTTGCAAGGGTCATTGCTTCCTGATGCATGTTTAACTGTCCTG >>>>>>>>>>>>>>>>>>>> 61 TGTTCACTTTGTTGCcGCAGGTTTTTAGAGGAACGTAAAGAGATCaCCGAGAAATTCAGT                     <<<<< 121GCGGAACAAGATGCCTTCCTGCAGGAGGCCCAGGAGCAGCATGCCCGTGAGCTG <<<<<<<<<<<<<<<116) Whole sequence 

 rs10854482-rs2839261CCCTGCACACTGACCTGCATGCCCTCGTCACCTGCACTCTGCATGCTCACCATCTGACGGACTCCTGCGAcGGGCATGGGAAGGTCGCCGCCGCCGGCAGCCtTGCGAGCACTTTGGATGTGTGCACCCGGCATGCCAGGCCCGAGTCAACAGACTGGCCGACCTTGGCGTCCTG (SEQ ID NO: 337)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 338, 339) LEFT PRIMER 21 20 55.22 65.00 4.00 0.00GCCCTCGTCACCTGCACTCT RIGHT PRIMER 168 20 64.77 60.00 5.00 1.00CCAAGGTCGGCCAGTCTGTT SEQUENCE SIZE: 175 INCLUDED REGION SIZE: 175PRODUCT SIZE: 148, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 0.00   1CCCTGCACACTGACCTGCATGCCCTCGTCACCTGCACTCTGCATGCTCACCATCTGACGG       >>>>>>>>>>>>>>>>>>>>  61ACTCCTGCGAcGGGCATGGGAAGGTCGCCGCCGCCGGCAGCCtTGCGAGCACTTTGGATG 121TGTGCACCCGGCATGCCAGGCCCGAGTCAACAGACTGGCCGACCTTGGCGTCCTG          <<<<<<<<<<<<<<<<<<<< 117) Whole sequence 

 rs2032111-rs718496TTTATTGCTGAGTGGTATTCCATTTTATGGGTCCATTATAGTTTATTTGTCCAGACACTTCATGGAAaGACATCAGTGTTTCCtGTTTTTCAATCATAAATTGATGTTTAATTTTAAAATTTTGGAATTGTAGAAGAAATGCAATTCTTTTTTCC (SEQ ID NO: 340)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 341, 342) LEFT PRIMER 28 22 53.65 31.82 4.00 3.00TGGGTCCATTATAGTTTATTTG RIGHT PRIMER 143 22 57.46 31.82 4.00 3.00TGCATTTCTTCTACAATTCCAA SEQUENCE SIZE: 155 INCLUDED REGION SIZE: 155PRODUCT SIZE: 116, PAIR ANY COMPL: 5.00, PAIR 3′ COMPL: 3.00   1TTTATTGCTGAGTGGTATTCCATTTTATGGGTCCATTATAGTTTATTTGTCCAGACACTT          >>>>>>>>>>>>>>>>>>>>  61CATGGAAaGACATCAGTGTTTCCtGTTTTTCAATCATAAATTGATGTTTAATTTTAAAAT 121TTTGGAATTGTAGAAGAAATGCAATTCTTTTTTCC <<<<<<<<<<<<<<<<<<<<118) Whole sequence 

 rs2070434-rs2070435CTTTGGTGCAGAATCATGCTGCAGGCAAGGTGGGCCCACCTCCCTGGAATTTCATCCCCCcCGTCAGTTAAACCCATGGTGGTTTTATTTTCTAGGCCACCTGATCTGGGAGGACCACCTCCAAGAAAAGCAGTCCTaTCGATGAACGGTCTAAGTTATGGTGTTATCAGAGTGGATACTGAAGAAAAGTTGTCAGTCCTTACTGTTC (SEQ ID NO: 343)OLIGO start len tm gc % any http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www_results_help.cgi - PRIMER_THREE 3′seq (SEQ ID NOs: 344, 345) LEFT PRIMER 33 20 66.57 60.00 4.00 3.00GGCCCACCTCCCTGGAATTT RIGHT PRIMER 176 22 54.26 40.91 4.00 0.00TCCACTCTGATAACACCATAAC SEQUENCE SIZE: 

INCLUDED REGION SIZE: 

PRODUCT SIZE: 144, PAIR ANY COMPL: 4.00, PAIR 3′ COMPL: 1.00   1CTTTGGTGCAGAATCATGCTGCAGGCAAGGTGGGCCCACCTCCCTGGAATTTCATCCCCC            >>>>>>>>>>>>>>>>>>>>  61cCGTCAGTTAAACCCATGGTGGTTTTATTTTCTAGGCCACCTGATCTGGGAGGACCACCT 121CCAAGAAAAGCAGTCCTaTCGATGAACGGTCTAAGTTATGGTGTTATCAGAGTGGATACT            <<<<<<<<<<<<<<<<<<<< 181 GAAGAAAAGTTGTCAGTCCTTACTGTTC

indicates data missing or illegible when filed

Example 6 Determining whether a Fetus has Trisomy

The number of alleles and the relationship between the number ofmolecules for the alleles detected for a particular marker are used todetermine whether a fetus has trisomy. The results of such an exemplaryexperiment are depicted in FIG. 3, which is an example of a constantdenaturant capillary electrophoresis electropherogram output, where eachpeak represents the number of molecules of alleles for a marker detectedin a sample. As will be appreciated, the marker can be any marker ofinterest where the maternal genome is heterozygous for that marker andthe fetus inherits an allele from the father that is not present in thematernal genome. Although the following description is provided in termsof a single marker, it will be appreciated that in any of the methodsdescribed herein, multiple markers may be analyzed, and in someembodiments, multiple markers are analyzed simultaneously in amultiplexed reaction. In specific embodiments, the marker is a tandemSNP, and different alleles detected for this marker represent differenthaplotypes. In still further embodiments, the tandem SNP represents ashort haplotype.

The upper panel of FIG. 3A illustrates the output that would result froma maternal buccal swab, which will comprise maternal nucleic acids butno fetal nucleic acids, In some embodiments, the maternal genome isheterozygous for a particular marker, and in such embodiments, twoalleles will be detected in the maternal sample, and these alleles willbe present in a 1:1 ratio, which is represented in the electropherogramoutput as two peaks of equal area.

The lower panel of FIG. 3A illustrates the output that would result froma sample from a baby with trisomy, where the sample comprises fetalnucleic acids but no maternal nucleic acids. The electropherogram outputexpected from such a sample would show three peaks with areas in a ratioof 1:1:1 or two peaks with areas in a ratio of 2:1. These ratios in thefetal sample result from the fact that a fetus with trisomy would haveinherited a total of three alleles for a particular marker: two allelesfrom the mother and one from the father. If the maternal genome isheterozygous for the marker, three alleles would be detectable in thesample, and all three alleles would be present in the same numbers,resulting in a ratio of 1:1:1, as depicted in the first trace of thelower panel in FIG. 3A (labeled “Baby with trisomy”). If the maternalgenome is homozygous for the marker, the fetus with trisomy would stillhave inherited two alleles from the mother and one from the father, butonly two different alleles would be detected in the fetal sample, soonly two peaks would be in the output. However, the number of moleculesfor each allele (represented by the area of the peak) would be differentand the peaks would be in a 2:1 ratio, as shown in the last two tracesof the lower panel in FIG. 3A. Although the term “peak” is discussedherein in terms of electropherogram output, it will be appreciated thatthe ratios and relationships described herein apply to the output of anymodality that provides information on the number of molecular of anallele present in a sample.

Similar experiments can be conducted on a sample containing bothmaternal and fetal nucleic acids, and the ratio of the peaks (i.e., thenumber of molecules for the different alleles of a marker) can be usedto determine whether a fetus has trisomy. FIG. 3B shows theelectropherogram outputs expected from a sample containing both maternaland fetal nucleic acids, where the fetus has trisomy. In thisillustrated example, the maternal genome is heterozygous for the marker,and the paternal genome has an allele that is not present in thematernal genome. The third peak (also referred to herein as the“paternal peak”) in the fetal sample output represents the alleleinherited from the father (also referred to herein as the “paternalallele”). In the example illustrated in this figure, the paternal alleleis not present in the maternal genome. Thus, at informative markers, asample containing both maternal and fetal nucleic acids will containthree alleles: the two from the maternal genome and the one inherited bythe fetus from the paternal genome. The electropherogram output willshow larger peaks for the two alleles in the maternal genome than forthe allele from the paternal genome, because the sample containsmolecules of the two alleles from the maternal genome and from the fetalgenome (because the fetus inherited both alleles from the mother). Thethird peak for the paternal allele will be smaller, because the numberof molecules for that allele are only contributed by the fetal nucleicacids in the sample—that allele is not present in the maternal genome,so the overall number of molecules for the paternal allele will be lessthan the number of molecules for the maternal alleles. The presentinventors have found that in such a sample, the number of molecules forthe different alleles of the marker will be in a specific ratio if ababy has trisomy. In one embodiment, the ratios will be evident as twoequal peaks (the maternal peaks) and a third smaller (paternal) peak,that is, the ratio will be x:peak+x:peak+x (first trace of FIG. 3B), orthe ratio will be x:peak:peak+2x, where x is the area of the smallestpeak, which represents the number of molecules of the paternal allele,and peak, peak+x, and peak+2x represent the number of molecules of thematernal alleles (which will be the number of molecules of the allelesfrom the maternal nucleic acids and the number of molecules of thealleles from the fetal nucleic acids inherited from the mother). In afurther embodiment, the ratio is about x:peak+x:peak+x or aboutx:peak:peak+2x if the baby has trisomy. In a still further embodiment,the ratio is approximately x:peak+x:peak+x or about x:peak:peak+2x ifthe baby has trisomy. As used herein, the term “approximately”encompasses any variation that can still be tolerated by statisticaltests to separate the different ratios. Common tests for statisticalsignificance include, among others, t-test, ANOVA, Kruskal-Wallis,Wilcoxon, Mann-Whitney and odds ratio. In some embodiments, approximateratios mean that there is a variation in a range of ±10% to ±50%. Aswill be appreciated, such range in variation may include rangesincluding without limitation ±10% to ±45%, ±15% to ±40%, ±20% to ±35%,and ±25% to ±30%.

FIG. 3C shows the results expected if the fetus is normal (i.e., doesnot have trisomy). In the situation illustrated in FIG. 3C, the maternalgenome is heterozygous for the marker and the fetal allele inheritedfrom the father is not present in the maternal genome. Since the normalfetus will only have inherited one allele from the father and one allelefrom the mother, the three peaks would have different areas, but theseareas would be in a different ratio to each other than would be seen fora fetus with trisomy. For a normal fetus, the areas will in oneembodiment be in a ratio of peak:x:peak+x. As in FIG. 3B, “x” is thepaternal peak and represents the number of molecules of the alleleinherited by the fetus from the father, and “peak” and “peak+x” are thematernal peaks and represent the number of molecules of the alleles inthe maternal genome and the number of molecules of the alleles in thefetal genome inherited from the mother. In a further embodiment, theareas will be in a ratio of about peak:x:peak+x. In a still furtherembodiment, the areas will be in ratio of approximately peak:x:peak+x.Since the fetus only inherited one allele from the mother, one of thematernal peaks would be larger than the other, and the larger peak wouldbe larger by the number “x”, because for the fetal nucleic acids in thesample, the number of molecules for the allele inherited from the fatherwill be the same as the number of molecules for the allele inheritedfrom the mother. The third paternal peak thus serves as an internalstandard of the number of molecules for alleles present in the fetalgenome, and the methods of the present invention do not require acomparison of measurements across different chromosomes. Detection ofalleles for a marker on a single chromosome can be used to detectwhether the fetus has a chromosomal abnormality. The third (paternal)peak serves as this internal sample whether the fetus has trisomy ornot, because this third peak represents only the molecules of the allelethe fetus inherited from the father. Since the paternal allele is notpresent in the maternal genome, the third peak is an internal standardthat is independent of the overall concentration of fetal nucleic acidsversus maternal nucleic acids in a particular sample.

All publications, patents and patent applications cited herein areincorporated herein by reference. While in the foregoing specificationthis invention has been described in relation to certain embodimentsthereof, and many details have been set forth for purposes ofillustration, it will be apparent to those skilled in the art that theinvention is susceptible to additional embodiments and that certain ofthe details described herein may be varied considerably withoutdeparting from the basic principles of the invention.

The use of the terms “a” and “an” and “the” and similar referents in thecontext of describing the invention are to be construed to cover boththe singular and the plural, unless otherwise indicated herein orclearly contradicted by context. The terms “comprising,” “having,”“including,” and “containing” are to be construed as open-ended terms(i.e., meaning “including, but not limited to”) unless otherwise noted.Recitation of ranges of values herein are merely intended to serve as ashorthand method of referring individually to each separate valuefalling within the range, unless otherwise indicated herein, and eachseparate value is incorporated into the specification as if it wereindividually recited herein. All methods described herein can beperformed in any suitable order unless otherwise indicated herein orotherwise clearly contradicted by context. The use of any and allexamples, or exemplary language (e.g., “such as”) provided herein, isintended merely to better illuminate the invention and does not pose alimitation on the scope of the invention unless otherwise claimed. Nolanguage in the specification should be construed as indicating anynon-claimed element as essential to the practice of the invention.

Embodiments of this invention are described herein, including the bestmode known to the inventors for carrying out the invention. Variationsof those embodiments may become apparent to those of ordinary skill inthe art upon reading the foregoing description. The inventors expectskilled artisans to employ such variations as appropriate, and theinventors intend for the invention to be practiced otherwise than asspecifically described herein. Accordingly, this invention includes allmodifications and equivalents of the subject matter recited in theclaims appended hereto as permitted by applicable law. Moreover, anycombination of the above-described elements in all possible variationsthereof is encompassed by the invention unless otherwise indicatedherein or otherwise clearly contradicted by context.

What is claimed is:
 1. A method for determining whether a fetus has apartial deletion, said method comprising: (a) providing a samplecomprising maternal and fetal cell free DNA; (b) designing primersdirected to alleles of interest comprising tandem single nucleotidepolymorphisms for specific chromosomal regions using computer software,wherein the alleles comprise tandem single nucleotide polymorphisms withsingle nucleotide polymorphisms that are at most 250 basepairs apart;(c) enriching the sample for the alleles of interest using the designedprimers to create isolated products; (d) sequencing the isolatedproducts; (e) detecting isolated products from the chromosomal region ofinterests that comprise at least three different alleles, wherein eachof the three different alleles of the chromosomal regions comprisedifferent haplotypes of the tandem SNP; (f) quantifying the detectedisolated products to calculate a haplotype ratio for the alleles ofinterest at the chromosomal regions of interest; and (g) determiningwhether the fetus has partial deletion based on the calculated haplotyperatios.
 2. The method of claim 1, wherein the deletion is a largedeletion.
 3. The method of claim 1, wherein the single nucleotidepolymorphisms in the tandem single nucleotide polymorphism are at most100 nucleotides apart.
 4. The method of claim 1, wherein the singlenucleotide polymorphisms in the tandem single nucleotide polymorphismare at most 75 nucleotides apart.
 5. The method of claim 1, wherein thesingle nucleotide polymorphisms in the tandem single nucleotidepolymorphism are at most 50 nucleotides apart.
 6. A method fordetermining whether a fetus has a partial insertion, said methodcomprising: (a) providing a sample comprising maternal and fetal cellfree DNA; (b) designing primers directed to alleles of interestcomprising tandem single nucleotide polymorphisms for specificchromosomal regions using computer software, wherein the allelescomprise tandem single nucleotide polymorphisms with single nucleotidepolymorphisms that are at most 250 basepairs apart; (c) enriching thesample for the alleles of interest using the designed primers to createisolated products; (d) sequencing the isolated products; (e) detectingisolated products from the chromosomal region of interests that compriseat least three different alleles, wherein each of the three differentalleles of the chromosomal regions comprise different haplotypes of thetandem SNP; (f) quantifying the detected isolated products to calculatea haplotype ratio for the alleles of interest at the chromosomal regionsof interest; and (g) determining whether the fetus has partial insertionbased on the calculated haplotype ratios.
 7. The method of claim 6,wherein the insertion is a large deletion.
 8. The method of claim 6,wherein the single nucleotide polymorphisms in the tandem singlenucleotide polymorphism are at most 100 nucleotides apart.
 9. The methodof claim 6, wherein the single nucleotide polymorphisms in the tandemsingle nucleotide polymorphism are at most 75 nucleotides apart.
 10. Themethod of claim 6, wherein the single nucleotide polymorphisms in thetandem single nucleotide polymorphism are at most 50 nucleotides apart.